From 96358ec9d3143ebe31f6b41f2790d2bb1b193123 Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Fri, 3 Apr 2020 14:57:28 -0700 Subject: [PATCH 01/13] ntedit: implement vcf output Former-commit-id: 27c91bd437a53ea04d93508ee872abb286a508cf --- ntedit.cpp | 76 +++++++++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 70 insertions(+), 6 deletions(-) diff --git a/ntedit.cpp b/ntedit.cpp index 7cc34c7..251e30e 100644 --- a/ntedit.cpp +++ b/ntedit.cpp @@ -7,6 +7,7 @@ #include #include #include +#include #include #include #include @@ -726,6 +727,7 @@ void writeEditsToFile( std::ofstream& dfout, std::ofstream& rfout, + std::ofstream& vfout, const std::string& contigHdr, const std::string& contigSeq, std::vector& newSeq, @@ -748,6 +750,10 @@ writeEditsToFile( if (!insertion_bases.empty()) { rfout << contigHdr.c_str() << "\t" << pos + 1 << "\t" << draft_char << "\t+" << insertion_bases.c_str() << "\t" << num_support << "\n"; + if (opt::snv) { + vfout << contigHdr.c_str() << "\t" << pos + 1 << "\t.\t" << draft_char << "\t" + << draft_char << insertion_bases.c_str() << "\t.\tPASS\tDP=" << num_support << "\n"; + } insertion_bases = ""; num_support = -1; } @@ -758,16 +764,35 @@ writeEditsToFile( << substitution_record.front().draft_char << "\t" << substitution_record.front().sub_base << "\t" << substitution_record.front().num_support; + std::string base(1, substitution_record.front().sub_base); + std::string support = ""; + support += std::to_string(substitution_record.front().num_support); if (substitution_record.front().altsupp1 > 0){//XXRLWXX rfout << "\t" << substitution_record.front().altbase1 << "\t" << substitution_record.front().altsupp1; + base += ","; + base += substitution_record.front().altbase1; + support += ","; + support += std::to_string(substitution_record.front().altsupp1); } if (substitution_record.front().altsupp2 > 0){//XXRLWXX rfout << "\t" << substitution_record.front().altbase2 << "\t" << substitution_record.front().altsupp2; + base += ","; + base += substitution_record.front().altbase2; + support += ","; + support += std::to_string(substitution_record.front().altsupp2); } if (substitution_record.front().altsupp3 > 0){//XXRLWXX rfout << "\t" << substitution_record.front().altbase3 << "\t" << substitution_record.front().altsupp3; + base += ","; + base += substitution_record.front().altbase3; + support += ","; + support += std::to_string(substitution_record.front().altsupp1); } rfout << "\n"; + if (opt::snv) { + vfout << contigHdr.c_str() << "\t" << substitution_record.front().pos + 1 << "\t.\t" << substitution_record.front().draft_char << "\t" + << base << "\t.\tPASS\tDP=" << support << "\n"; + } substitution_record.pop(); } // fprintf(dfout, "%s", contigSeq.substr(curr_node.s_pos, @@ -791,6 +816,11 @@ writeEditsToFile( rfout << contigHdr.c_str() << "\t" << pos + 1 << "\t" << contigSeq.at(pos) << "\t-" << contigSeq.substr(pos, (curr_node.s_pos - pos)).c_str() << "\t" << curr_node.num_support << "\n"; + if (opt::snv) { + vfout << contigHdr.c_str() << "\t" << pos << "\t.\t" << contigSeq.substr(pos-1, (curr_node.s_pos - pos)).c_str() << "\t" + << contigSeq.at(pos - 1) << "\t.\tPASS\tDP=" + << curr_node.num_support << "\n"; + } } } } @@ -1013,7 +1043,8 @@ tryDeletion( std::vector& newSeq, BloomFilter& bloom, BloomFilter& bloomrep, - std::string& deleted_bases) + std::string& deleted_bases, + std::string& prev_base) { // set temporary values @@ -1031,6 +1062,7 @@ tryDeletion( deleted_bases += getCharacter(temp_t_seq_i, newSeq[temp_t_node_index], contigSeq); increment(temp_t_seq_i, temp_t_node_index, newSeq); } + prev_base = getCharacter(temp_t_seq_i, newSeq[temp_t_node_index], contigSeq); NTMC64_changelast( draft_char, getCharacter(temp_t_seq_i, newSeq[temp_t_node_index], contigSeq), @@ -1192,6 +1224,7 @@ tryIndels( if (num_deletions <= opt::max_deletions) { std::string deleted_bases; + std::string prev_base; unsigned del_support = tryDeletion( draft_char, num_deletions, @@ -1206,7 +1239,8 @@ tryIndels( newSeq, bloom, bloomrep, - deleted_bases); + deleted_bases, + prev_base); if (del_support > 0) { if (opt::mode == 0) { best_edit_type = 3; @@ -1253,7 +1287,8 @@ kmerizeAndCorrect( BloomFilter& bloom, BloomFilter& bloomrep, std::ofstream& dfout, - std::ofstream& rfout) + std::ofstream& rfout, + std::ofstream& vfout) { // initialize values for hashing @@ -1583,7 +1618,7 @@ kmerizeAndCorrect( #pragma omp critical(write) { // write this to file - writeEditsToFile(dfout, rfout, contigHdr, contigSeq, newSeq, substitution_record); + writeEditsToFile(dfout, rfout, vfout, contigHdr, contigSeq, newSeq, substitution_record); } } @@ -1601,8 +1636,10 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) // outfile handles std::string d_filename = opt::outfile_prefix + "_edited.fa"; std::string r_filename = opt::outfile_prefix + "_changes.tsv"; + std::string v_filename = opt::outfile_prefix + "_variants.vcf"; ofstream dfout; ofstream rfout; + ofstream vfout; dfout.open(d_filename); rfout.open(r_filename); //printf ( "OUT OF %.1f\n", ceil( double(opt::k) / double(opt::jump) ) ); @@ -1611,7 +1648,31 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) << ceil( double(opt::k) / double(opt::jump)) << ")\tAlt.Base1\tAlt.Support1\t" << "Alt.Base2\tAlt.Support2\tAlt.Base3\tAlt.Support3\n"; // RLW -#pragma omp parallel shared(seq, dfout, rfout) + if (opt::snv) { + vfout.open(v_filename); + + vfout << "##fileformat=VCFv4.2" << std::endl; + + time_t now = time(0); + tm *ltm = localtime(&now); + std::string year = std::to_string(1900 + ltm->tm_year); + std::string month = std::to_string(1 + ltm->tm_mon); + if (month.size() < 2) { + month.insert(0, "0"); + } + std::string day = std::to_string(ltm->tm_mday); + if (day.size() < 2) { + day.insert(0, "0"); + } + + vfout << "##fileDate=" << year << month << day << std::endl; + vfout << "##source=ntEditV1.3.2" << std::endl; + vfout << "##reference=file:" << opt::draft_filename <" << std::endl; + vfout << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" << std::endl; + } + +#pragma omp parallel shared(seq, dfout, rfout, vfout) { std::string contigHdr; std::string contigSeq; @@ -1641,7 +1702,7 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) std::cout << contigName << std::endl; } if (seq_len >= opt::min_contig_len) { - kmerizeAndCorrect(contigName, contigSeq, seq_len, bloom, bloomrep, dfout, rfout); + kmerizeAndCorrect(contigName, contigSeq, seq_len, bloom, bloomrep, dfout, rfout, vfout); } #pragma omp atomic num_contigs++; @@ -1655,6 +1716,9 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) gzclose(dfp); dfout.close(); rfout.close(); + if (opt::snv) { + vfout.close(); + } } int From 300835b4d2d732c69eb2b3a005c25368f2241561 Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Fri, 3 Apr 2020 15:02:50 -0700 Subject: [PATCH 02/13] ntedit: remove unnecessary code Former-commit-id: 85dac8d7f16fc33bdf31c1c855444050d0cf4f9c --- ntedit.cpp | 58 +++++++++++++++++++++++++----------------------------- 1 file changed, 27 insertions(+), 31 deletions(-) diff --git a/ntedit.cpp b/ntedit.cpp index 251e30e..c523983 100644 --- a/ntedit.cpp +++ b/ntedit.cpp @@ -727,7 +727,7 @@ void writeEditsToFile( std::ofstream& dfout, std::ofstream& rfout, - std::ofstream& vfout, + std::ofstream& vfout, const std::string& contigHdr, const std::string& contigSeq, std::vector& newSeq, @@ -1043,8 +1043,7 @@ tryDeletion( std::vector& newSeq, BloomFilter& bloom, BloomFilter& bloomrep, - std::string& deleted_bases, - std::string& prev_base) + std::string& deleted_bases) { // set temporary values @@ -1062,7 +1061,6 @@ tryDeletion( deleted_bases += getCharacter(temp_t_seq_i, newSeq[temp_t_node_index], contigSeq); increment(temp_t_seq_i, temp_t_node_index, newSeq); } - prev_base = getCharacter(temp_t_seq_i, newSeq[temp_t_node_index], contigSeq); NTMC64_changelast( draft_char, getCharacter(temp_t_seq_i, newSeq[temp_t_node_index], contigSeq), @@ -1224,7 +1222,6 @@ tryIndels( if (num_deletions <= opt::max_deletions) { std::string deleted_bases; - std::string prev_base; unsigned del_support = tryDeletion( draft_char, num_deletions, @@ -1239,8 +1236,7 @@ tryIndels( newSeq, bloom, bloomrep, - deleted_bases, - prev_base); + deleted_bases); if (del_support > 0) { if (opt::mode == 0) { best_edit_type = 3; @@ -1288,7 +1284,7 @@ kmerizeAndCorrect( BloomFilter& bloomrep, std::ofstream& dfout, std::ofstream& rfout, - std::ofstream& vfout) + std::ofstream& vfout) { // initialize values for hashing @@ -1648,29 +1644,29 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) << ceil( double(opt::k) / double(opt::jump)) << ")\tAlt.Base1\tAlt.Support1\t" << "Alt.Base2\tAlt.Support2\tAlt.Base3\tAlt.Support3\n"; // RLW - if (opt::snv) { - vfout.open(v_filename); - - vfout << "##fileformat=VCFv4.2" << std::endl; + if (opt::snv) { + vfout.open(v_filename); + + vfout << "##fileformat=VCFv4.2" << std::endl; - time_t now = time(0); - tm *ltm = localtime(&now); + time_t now = time(0); + tm *ltm = localtime(&now); std::string year = std::to_string(1900 + ltm->tm_year); std::string month = std::to_string(1 + ltm->tm_mon); - if (month.size() < 2) { - month.insert(0, "0"); - } - std::string day = std::to_string(ltm->tm_mday); - if (day.size() < 2) { - day.insert(0, "0"); - } - - vfout << "##fileDate=" << year << month << day << std::endl; - vfout << "##source=ntEditV1.3.2" << std::endl; - vfout << "##reference=file:" << opt::draft_filename <" << std::endl; - vfout << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" << std::endl; - } + if (month.size() < 2) { + month.insert(0, "0"); + } + std::string day = std::to_string(ltm->tm_mday); + if (day.size() < 2) { + day.insert(0, "0"); + } + + vfout << "##fileDate=" << year << month << day << std::endl; + vfout << "##source=ntEditV1.3.2" << std::endl; + vfout << "##reference=file:" << opt::draft_filename <" << std::endl; + vfout << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" << std::endl; + } #pragma omp parallel shared(seq, dfout, rfout, vfout) { @@ -1716,9 +1712,9 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) gzclose(dfp); dfout.close(); rfout.close(); - if (opt::snv) { - vfout.close(); - } + if (opt::snv) { + vfout.close(); + } } int From 4e7c7a0f8020d6d104e0648d34786e7a6b3c3d74 Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Fri, 3 Apr 2020 15:14:41 -0700 Subject: [PATCH 03/13] ntedit: clang-format Former-commit-id: 232dd672b409d0a7304a960db0354f39e4086faf --- ntedit.cpp | 295 ++++++++++++++++++++++++++++++----------------------- 1 file changed, 165 insertions(+), 130 deletions(-) diff --git a/ntedit.cpp b/ntedit.cpp index c523983..6258976 100644 --- a/ntedit.cpp +++ b/ntedit.cpp @@ -44,31 +44,37 @@ static const char USAGE_MESSAGE[] = PROGRAM " -t, number of threads [default=1]\n" " -f, draft genome assembly (FASTA, Multi-FASTA, and/or gzipped compatible), REQUIRED\n" " -r, Bloom filter file (generated from ntHits), REQUIRED\n" - " -e, secondary Bloom filter with kmers to reject (generated from ntHits), OPTIONAL. EXPERIMENTAL\n" + " -e, secondary Bloom filter with kmers to reject (generated from ntHits), OPTIONAL. " + "EXPERIMENTAL\n" " -b, output file prefix, OPTIONAL\n" " -z, minimum contig length [default=100]\n" " -i, maximum number of insertion bases to try, range 0-5, [default=4]\n" " -d, maximum number of deletions bases to try, range 0-5, [default=5]\n" " -x, k/x ratio for the number of kmers that should be missing, [default=5.000]\n" " -y, k/y ratio for the number of editted kmers that should be present, [default=9.000]\n" - " -X, ratio of number of kmers in the k subset that should be missing in order to attempt fix (higher=stringent), [default=0.5]\n" - " -Y, ratio of number of kmers in the k subset that should be present to accept an edit (higher=stringent), [default=0.5]\n" - " -c, cap for the number of base insertions that can be made at one position, [default=k*1.5]\n" - " -j, controls size of kmer subset. When checking subset of kmers, check every jth kmer, [default=3]\n" + " -X, ratio of number of kmers in the k subset that should be missing in order to " + "attempt fix (higher=stringent), [default=0.5]\n" + " -Y, ratio of number of kmers in the k subset that should be present to accept an edit " + "(higher=stringent), [default=0.5]\n" + " -c, cap for the number of base insertions that can be made at one position, " + "[default=k*1.5]\n" + " -j, controls size of kmer subset. When checking subset of kmers, check every jth kmer, " + "[default=3]\n" " -m, mode of editing, range 0-2, [default=0]\n" " 0: best substitution, or first good indel\n" " 1: best substitution, or best indel\n" " 2: best edit overall (suggestion that you reduce i and d for performance)\n" - " -s, SNV mode. Overrides draft kmer checks, forcing reassessment at each position (-s 1 = yes, default = 0, no. EXPERIMENTAL)\n" + " -s, SNV mode. Overrides draft kmer checks, forcing reassessment at each position (-s 1 " + "= yes, default = 0, no. EXPERIMENTAL)\n" " -v, verbose mode (-v 1 = yes, default = 0, no)\n" "\n" " --help, display this message and exit \n" " --version, output version information and exit\n" "\n" - " If one of X/Y is set, ntEdit will use those parameters instead. Otherwise, it uses x/y by default.\n" + " If one of X/Y is set, ntEdit will use those parameters instead. Otherwise, it uses x/y by " + "default.\n" "\n"; - namespace opt { /* Defining magical numbers. */ constexpr int default_min_contig_len = 100; @@ -82,10 +88,10 @@ float missing_ratio = 0.5; bool use_ratio = false; unsigned jump = 3; unsigned nthreads = 1; -std::string draft_filename; // NOLINT -std::string bloom_filename; // NOLINT +std::string draft_filename; // NOLINT +std::string bloom_filename; // NOLINT std::string bloomrep_filename; // NOLINT -std::string outfile_prefix; // NOLINT +std::string outfile_prefix; // NOLINT unsigned k; unsigned h = 0; unsigned e = 0; @@ -126,7 +132,7 @@ static const struct option longopts[] = { { "bloomrep_filename", required_argument, nullptr, 'e' }, { "outfile_prefix", required_argument, nullptr, 'b' }, { "mode", required_argument, nullptr, 'm' }, - { "snv", required_argument, nullptr, 's' }, + { "snv", required_argument, nullptr, 's' }, { "verbose", required_argument, nullptr, 'v' }, { "help", no_argument, nullptr, OPT_HELP }, { "version", no_argument, nullptr, OPT_VERSION }, @@ -750,10 +756,11 @@ writeEditsToFile( if (!insertion_bases.empty()) { rfout << contigHdr.c_str() << "\t" << pos + 1 << "\t" << draft_char << "\t+" << insertion_bases.c_str() << "\t" << num_support << "\n"; - if (opt::snv) { - vfout << contigHdr.c_str() << "\t" << pos + 1 << "\t.\t" << draft_char << "\t" - << draft_char << insertion_bases.c_str() << "\t.\tPASS\tDP=" << num_support << "\n"; - } + + vfout << contigHdr.c_str() << "\t" << pos + 1 << "\t.\t" << draft_char << "\t" + << draft_char << insertion_bases.c_str() << "\t.\tPASS\tDP=" << num_support + << "\n"; + insertion_bases = ""; num_support = -1; } @@ -765,34 +772,38 @@ writeEditsToFile( << substitution_record.front().sub_base << "\t" << substitution_record.front().num_support; std::string base(1, substitution_record.front().sub_base); - std::string support = ""; + std::string support = ""; support += std::to_string(substitution_record.front().num_support); - if (substitution_record.front().altsupp1 > 0){//XXRLWXX - rfout << "\t" << substitution_record.front().altbase1 << "\t" << substitution_record.front().altsupp1; + if (substitution_record.front().altsupp1 > 0) { // XXRLWXX + rfout << "\t" << substitution_record.front().altbase1 << "\t" + << substitution_record.front().altsupp1; base += ","; base += substitution_record.front().altbase1; support += ","; support += std::to_string(substitution_record.front().altsupp1); } - if (substitution_record.front().altsupp2 > 0){//XXRLWXX - rfout << "\t" << substitution_record.front().altbase2 << "\t" << substitution_record.front().altsupp2; + if (substitution_record.front().altsupp2 > 0) { // XXRLWXX + rfout << "\t" << substitution_record.front().altbase2 << "\t" + << substitution_record.front().altsupp2; base += ","; base += substitution_record.front().altbase2; support += ","; support += std::to_string(substitution_record.front().altsupp2); } - if (substitution_record.front().altsupp3 > 0){//XXRLWXX - rfout << "\t" << substitution_record.front().altbase3 << "\t" << substitution_record.front().altsupp3; + if (substitution_record.front().altsupp3 > 0) { // XXRLWXX + rfout << "\t" << substitution_record.front().altbase3 << "\t" + << substitution_record.front().altsupp3; base += ","; base += substitution_record.front().altbase3; support += ","; support += std::to_string(substitution_record.front().altsupp1); } rfout << "\n"; - if (opt::snv) { - vfout << contigHdr.c_str() << "\t" << substitution_record.front().pos + 1 << "\t.\t" << substitution_record.front().draft_char << "\t" - << base << "\t.\tPASS\tDP=" << support << "\n"; - } + + vfout << contigHdr.c_str() << "\t" << substitution_record.front().pos + 1 << "\t.\t" + << substitution_record.front().draft_char << "\t" << base + << "\t.\tPASS\tDP=" << support << "\n"; + substitution_record.pop(); } // fprintf(dfout, "%s", contigSeq.substr(curr_node.s_pos, @@ -816,15 +827,14 @@ writeEditsToFile( rfout << contigHdr.c_str() << "\t" << pos + 1 << "\t" << contigSeq.at(pos) << "\t-" << contigSeq.substr(pos, (curr_node.s_pos - pos)).c_str() << "\t" << curr_node.num_support << "\n"; - if (opt::snv) { - vfout << contigHdr.c_str() << "\t" << pos << "\t.\t" << contigSeq.substr(pos-1, (curr_node.s_pos - pos)).c_str() << "\t" - << contigSeq.at(pos - 1) << "\t.\tPASS\tDP=" - << curr_node.num_support << "\n"; - } + + vfout << contigHdr.c_str() << "\t" << pos << "\t.\t" + << contigSeq.substr(pos - 1, (curr_node.s_pos - pos)).c_str() << "\t" + << contigSeq.at(pos - 1) << "\t.\tPASS\tDP=" << curr_node.num_support << "\n"; } } } - dfout << "\n";//FASTA RECORD + dfout << "\n"; // FASTA RECORD } /* Roll ntHash using the seqNode structure. */ @@ -899,7 +909,7 @@ makeEdit( subst.num_support = best_num_support; if (altsupp1 && altbase1 != best_sub_base) { subst.altbase1 = altbase1; - subst.altsupp1 = altsupp1; + subst.altsupp1 = altsupp1; } if (altsupp2 && altbase2 != altbase1) { subst.altbase2 = altbase2; @@ -1086,7 +1096,8 @@ tryDeletion( charOut, charIn)) { NTMC64(charOut, charIn, opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); - if (k%opt::jump == 0 && bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) { + if (k % opt::jump == 0 && bloom.contains(hVal) && + (!opt::secbf || !bloomrep.contains(hVal))) { check_present++; } } @@ -1096,8 +1107,11 @@ tryDeletion( std::cout << "\t\tdeleting: " << deleted_bases << " check_present: " << check_present << std::endl; } - if ((!opt::use_ratio && static_cast(check_present) >= ( static_cast(opt::k) / opt::edit_threshold)) - || (opt::use_ratio && static_cast(check_present) >= ( 1 + ( static_cast(opt::k) / opt::jump )) * opt::edit_ratio)) { // RLW + if ((!opt::use_ratio && + static_cast(check_present) >= (static_cast(opt::k) / opt::edit_threshold)) || + (opt::use_ratio && + static_cast(check_present) >= + (1 + (static_cast(opt::k) / opt::jump)) * opt::edit_ratio)) { // RLW return static_cast(check_present); } return 0; @@ -1164,14 +1178,15 @@ tryIndels( for (; k < insertion_bases.size() - 1 && temp_h_seq_i < contigSeq.size(); k++) { NTMC64( getCharacter(temp_h_seq_i, newSeq[temp_h_node_index], contigSeq), - insertion_bases[k+1], + insertion_bases[k + 1], opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); increment(temp_h_seq_i, temp_h_node_index, newSeq); - if (k % opt::jump == 0 && bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) {// RLW + if (k % opt::jump == 0 && bloom.contains(hVal) && + (!opt::secbf || !bloomrep.contains(hVal))) { // RLW check_present++; } } @@ -1187,7 +1202,8 @@ tryIndels( charOut, charIn)) { NTMC64(charOut, charIn, opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); - if (k % opt::jump == 0 && bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) {//RLW + if (k % opt::jump == 0 && bloom.contains(hVal) && + (!opt::secbf || !bloomrep.contains(hVal))) { // RLW check_present++; } } @@ -1198,7 +1214,11 @@ tryIndels( << std::endl; } // if the insertion is good, store the insertion accordingly RLW - if ((!opt::use_ratio && static_cast(check_present) >= (static_cast(opt::k) / opt::edit_threshold)) || (opt::use_ratio && static_cast(check_present) >= ( static_cast(opt::k) / opt::jump) * opt::edit_ratio)) { // RLW + if ((!opt::use_ratio && static_cast(check_present) >= + (static_cast(opt::k) / opt::edit_threshold)) || + (opt::use_ratio && + static_cast(check_present) >= + (static_cast(opt::k) / opt::jump) * opt::edit_ratio)) { // RLW if (opt::mode == 0) { // if we are in default mode, we just accept this first good insertion and return best_edit_type = 2; @@ -1209,7 +1229,7 @@ tryIndels( if (opt::mode == 1 || opt::mode == 2) { // if we are in some deep mode, we look for the best indel within index char first if (check_present >= temp_best_num_support) { - if(temp_best_num_support) { + if (temp_best_num_support) { temp_alt_indel = temp_best_indel; temp_alt_num_support = temp_best_num_support; } @@ -1246,7 +1266,7 @@ tryIndels( } if (opt::mode == 1 || opt::mode == 2) { if (del_support >= temp_best_num_support) { - if(temp_best_num_support) { + if (temp_best_num_support) { temp_alt_indel = temp_best_indel; temp_alt_num_support = temp_best_num_support; } @@ -1349,7 +1369,8 @@ kmerizeAndCorrect( unsigned check_missing = 0; unsigned check_there = 0; // RLW bool do_not_fix = false; - for (unsigned k = 0; k < opt::k && temp_h_seq_i < seqLen; k++) { // RLW -- below roll may be adjusted/dupli to account for gapped seed + for (unsigned k = 0; k < opt::k && temp_h_seq_i < seqLen; + k++) { // RLW -- below roll may be adjusted/dupli to account for gapped seed if (roll( temp_h_seq_i, temp_t_seq_i, @@ -1366,8 +1387,7 @@ kmerizeAndCorrect( } if (k % opt::jump == 0 && !bloom.contains(hVal)) { // RLW check_missing++; - } - else if(k % opt::jump == 0 && bloom.contains(hVal)){ // XXRLWXX + } else if (k % opt::jump == 0 && bloom.contains(hVal)) { // XXRLWXX check_there++; } } else { @@ -1379,8 +1399,13 @@ kmerizeAndCorrect( if (opt::verbose) { std::cout << "\tcheck_missing: " << check_missing << std::endl; } - if ((opt::snv) || ((!do_not_fix) && (((!opt::use_ratio && static_cast(check_missing) >= (static_cast(opt::k) / opt::missing_threshold))) - || ((opt::use_ratio && static_cast(check_missing) >= (( static_cast(opt::k) / opt::jump) * opt::missing_ratio)))))) { // RLW + if ((opt::snv) || ((!do_not_fix) && + (((!opt::use_ratio && + static_cast(check_missing) >= + (static_cast(opt::k) / opt::missing_threshold))) || + ((opt::use_ratio && static_cast(check_missing) >= + ((static_cast(opt::k) / opt::jump) * + opt::missing_ratio)))))) { // RLW // recorders unsigned num_deletions = 1; @@ -1393,23 +1418,27 @@ kmerizeAndCorrect( unsigned char altbase1; unsigned char altbase2; unsigned char altbase3; - unsigned altsupp1 = 0; + unsigned altsupp1 = 0; unsigned altsupp2 = 0; unsigned altsupp3 = 0; - if(opt::snv){ // XXRLWXX -- sets baseline for draft + if (opt::snv) { // XXRLWXX -- sets baseline for draft - if ((!opt::use_ratio && static_cast(check_there) >= (static_cast(opt::k) / opt::edit_threshold)) - || (opt::use_ratio && static_cast(check_there) >= (( static_cast(opt::k) / opt::jump))*opt::edit_ratio)) { + if ((!opt::use_ratio && + static_cast(check_there) >= + (static_cast(opt::k) / opt::edit_threshold)) || + (opt::use_ratio && + static_cast(check_there) >= + ((static_cast(opt::k) / opt::jump)) * opt::edit_ratio)) { best_sub_base = draft_char; best_num_support = check_there; if (opt::verbose) { std::cout << "\t\tORI BEST SUB BASE: " << best_sub_base - << " NUMBER: " << best_num_support << std::endl; + << " NUMBER: " << best_num_support << std::endl; } } - } + } // try substitution for (const unsigned char sub_base : bases_array[draft_char]) { @@ -1422,7 +1451,8 @@ kmerizeAndCorrect( draft_char, sub_base, opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); // only do verification of substitution if it is found in Bloom filter - if ((bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) || opt::mode == 2) { + if ((bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) || + opt::mode == 2) { // reset temporary values temp_h_node_index = h_node_index; temp_t_node_index = t_node_index; @@ -1451,7 +1481,8 @@ kmerizeAndCorrect( charIn)) { NTMC64( charOut, charIn, opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); - if (k % opt::jump == 0 && bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) { // RLW + if (k % opt::jump == 0 && bloom.contains(hVal) && + (!opt::secbf || !bloomrep.contains(hVal))) { // RLW check_present++; } } else { @@ -1470,8 +1501,12 @@ kmerizeAndCorrect( << " check_present: " << check_present << std::endl; } - if ((!opt::use_ratio && static_cast(check_present) >= (static_cast(opt::k) / opt::edit_threshold)) - || (opt::use_ratio && static_cast(check_present) >= (( static_cast(opt::k) / opt::jump))*opt::edit_ratio)) { // RLW + if ((!opt::use_ratio && + static_cast(check_present) >= + (static_cast(opt::k) / opt::edit_threshold)) || + (opt::use_ratio && static_cast(check_present) >= + ((static_cast(opt::k) / opt::jump)) * + opt::edit_ratio)) { // RLW // update the best substitution if (check_present >= best_num_support) { @@ -1479,22 +1514,22 @@ kmerizeAndCorrect( altbase3 = altbase2; altsupp3 = altsupp2; } - if(altsupp1) { + if (altsupp1) { altbase2 = altbase1; altsupp2 = altsupp1; } - if(best_num_support) { + if (best_num_support) { altsupp1 = best_num_support; altbase1 = best_sub_base; } best_edit_type = 1; best_sub_base = sub_base; best_num_support = check_present; - } else{ - if (! altsupp1) { + } else { + if (!altsupp1) { altbase1 = sub_base; altsupp1 = check_present; - } else if (! altsupp2) { + } else if (!altsupp2) { if (check_present < altsupp1) { altbase2 = sub_base; altsupp2 = check_present; @@ -1504,7 +1539,7 @@ kmerizeAndCorrect( altbase1 = sub_base; altsupp1 = check_present; } - } else if (! altsupp3) { + } else if (!altsupp3) { if (check_present < altsupp2) { altbase3 = sub_base; altsupp3 = check_present; @@ -1546,7 +1581,7 @@ kmerizeAndCorrect( contigSeq, newSeq, bloom, - bloomrep, + bloomrep, best_edit_type, best_indel, alt_indel, @@ -1638,35 +1673,33 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) ofstream vfout; dfout.open(d_filename); rfout.open(r_filename); - //printf ( "OUT OF %.1f\n", ceil( double(opt::k) / double(opt::jump) ) ); + // printf ( "OUT OF %.1f\n", ceil( double(opt::k) / double(opt::jump) ) ); rfout << "ID\tbpPosition+1\tOriginalBase\tNewBase\tSupport " << opt::k << "-mer (out of " - << ceil( double(opt::k) / double(opt::jump)) << ")\tAlt.Base1\tAlt.Support1\t" + << ceil(double(opt::k) / double(opt::jump)) << ")\tAlt.Base1\tAlt.Support1\t" << "Alt.Base2\tAlt.Support2\tAlt.Base3\tAlt.Support3\n"; // RLW - if (opt::snv) { - vfout.open(v_filename); - - vfout << "##fileformat=VCFv4.2" << std::endl; - - time_t now = time(0); - tm *ltm = localtime(&now); - std::string year = std::to_string(1900 + ltm->tm_year); - std::string month = std::to_string(1 + ltm->tm_mon); - if (month.size() < 2) { - month.insert(0, "0"); - } - std::string day = std::to_string(ltm->tm_mday); - if (day.size() < 2) { - day.insert(0, "0"); - } - - vfout << "##fileDate=" << year << month << day << std::endl; - vfout << "##source=ntEditV1.3.2" << std::endl; - vfout << "##reference=file:" << opt::draft_filename <" << std::endl; - vfout << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" << std::endl; - } + vfout.open(v_filename); + + vfout << "##fileformat=VCFv4.2" << std::endl; + + time_t now = time(0); + tm* ltm = localtime(&now); + std::string year = std::to_string(1900 + ltm->tm_year); + std::string month = std::to_string(1 + ltm->tm_mon); + if (month.size() < 2) { + month.insert(0, "0"); + } + std::string day = std::to_string(ltm->tm_mday); + if (day.size() < 2) { + day.insert(0, "0"); + } + + vfout << "##fileDate=" << year << month << day << std::endl; + vfout << "##source=ntEditV1.3.2" << std::endl; + vfout << "##reference=file:" << opt::draft_filename << std::endl; + vfout << "##FORMAT=" << std::endl; + vfout << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" << std::endl; #pragma omp parallel shared(seq, dfout, rfout, vfout) { @@ -1698,7 +1731,8 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) std::cout << contigName << std::endl; } if (seq_len >= opt::min_contig_len) { - kmerizeAndCorrect(contigName, contigSeq, seq_len, bloom, bloomrep, dfout, rfout, vfout); + kmerizeAndCorrect( + contigName, contigSeq, seq_len, bloom, bloomrep, dfout, rfout, vfout); } #pragma omp atomic num_contigs++; @@ -1712,9 +1746,7 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) gzclose(dfp); dfout.close(); rfout.close(); - if (opt::snv) { - vfout.close(); - } + vfout.close(); } int @@ -1759,11 +1791,11 @@ main(int argc, char** argv) break; case 'X': arg >> opt::missing_ratio; - opt::use_ratio=true; + opt::use_ratio = true; break; case 'Y': arg >> opt::edit_ratio; - opt::use_ratio=true; + opt::use_ratio = true; break; case 'c': arg >> opt::insertion_cap; @@ -1821,7 +1853,7 @@ main(int argc, char** argv) // check that the repeat bloom filter file is specified - RLW2019 if (opt::bloomrep_filename.empty()) { - opt::secbf = 0;//flag will track whether to query secondary Bloom filter or not + opt::secbf = 0; // flag will track whether to query secondary Bloom filter or not } else { // if the file is specified check that it is readable opt::secbf = 1; @@ -1834,10 +1866,11 @@ main(int argc, char** argv) } // added nov21 2019 XXRLW - if(opt::snv){ + if (opt::snv) { opt::max_insertions = 0; opt::max_deletions = 0; - std::cerr << PROGRAM ": EXPERIMENTAL feature note: i and d set to 0 when s is set to 1; Only tracking single-base variants.\n"; + std::cerr << PROGRAM ": EXPERIMENTAL feature note: i and d set to 0 when s is set to 1; " + "Only tracking single-base variants.\n"; } // get the basename for the file @@ -1853,7 +1886,8 @@ main(int argc, char** argv) // Load bloom filter time(&rawtime); - std::cout << "---------- loading Bloom filter from file : " << ctime(&rawtime) << "\n"; + std::cout << "---------- loading Bloom filter from file : " << ctime(&rawtime) + << "\n"; BloomFilter bloom(opt::bloom_filename.c_str()); opt::h = bloom.getHashNum(); @@ -1866,13 +1900,14 @@ main(int argc, char** argv) // assign k from Bloom filter header opt::k = bloom.getKmerSize(); - opt::insertion_cap = static_cast(static_cast(opt::k) * opt::default_insertion_cap_ratio); + opt::insertion_cap = + static_cast(static_cast(opt::k) * opt::default_insertion_cap_ratio); // print bloom filter details bloom.printBloomFilterDetails(); // Checking parameters - time(&rawtime); + time(&rawtime); std::cout << "\n---------- verifying parameters : " << ctime(&rawtime); // check that the parameters x and y are in bound if (opt::missing_threshold < 3 && opt::missing_threshold > static_cast(opt::k) && @@ -1903,10 +1938,10 @@ main(int argc, char** argv) } // print parameters: - std::cout << "\nrunning : " << PROGRAM << "\n -f " << draft_basename - << "\n -k " << opt::k << "\n -z " << opt::min_contig_len << "\n -b " - << opt::outfile_prefix << "\n -r " << bloom_basename << "\n -e " << bloomrep_basename - << "\n -i " << opt::max_insertions << "\n -d " << opt::max_deletions; + std::cout << "\nrunning : " << PROGRAM << "\n -f " << draft_basename << "\n -k " << opt::k + << "\n -z " << opt::min_contig_len << "\n -b " << opt::outfile_prefix << "\n -r " + << bloom_basename << "\n -e " << bloomrep_basename << "\n -i " << opt::max_insertions + << "\n -d " << opt::max_deletions; if (opt::use_ratio) { // RLW std::cout << "\n -X " << opt::missing_ratio << "\n -Y " << opt::edit_ratio; @@ -1914,43 +1949,43 @@ main(int argc, char** argv) std::cout << "\n -x " << opt::missing_threshold << "\n -y " << opt::edit_threshold; } - std::cout << "\n -j " << opt::jump << "\n -m " << opt::mode - << "\n -s " << opt::snv << "\n -t " << opt::nthreads << "\n -v " << opt::verbose << "\n" << std::endl; + std::cout << "\n -j " << opt::jump << "\n -m " << opt::mode << "\n -s " << opt::snv << "\n -t " + << opt::nthreads << "\n -v " << opt::verbose << "\n" + << std::endl; // Read & edit contigs time(&rawtime); if (opt::secbf) { time(&rawtime); - std::cout << "---------- loading secondary Bloom filter from file : " << ctime(&rawtime) << "\n"; - BloomFilter bloomrep(opt::bloomrep_filename.c_str()); - opt::e = bloomrep.getHashNum(); - - // Checks for the Bloom filter - if (opt::e == 0) { - std::cerr << PROGRAM ": error: secondary Bloom filter file supplied (-e) is incorrect.\n"; - exit(EXIT_FAILURE); - } + std::cout << "---------- loading secondary Bloom filter from file : " << ctime(&rawtime) + << "\n"; + BloomFilter bloomrep(opt::bloomrep_filename.c_str()); + opt::e = bloomrep.getHashNum(); + + // Checks for the Bloom filter + if (opt::e == 0) { + std::cerr << PROGRAM + ": error: secondary Bloom filter file supplied (-e) is incorrect.\n"; + exit(EXIT_FAILURE); + } // Check that primary and secondary BF kmer sizes match - if (opt::k != bloomrep.getKmerSize()) { - std::cerr << PROGRAM ": error: secondary Bloom filter k size (" - << bloomrep.getKmerSize() - << ") is different than main Bloom filter k size (" - << opt::k - << ")\n"; - exit(EXIT_FAILURE); - } + if (opt::k != bloomrep.getKmerSize()) { + std::cerr << PROGRAM ": error: secondary Bloom filter k size (" + << bloomrep.getKmerSize() << ") is different than main Bloom filter k size (" + << opt::k << ")\n"; + exit(EXIT_FAILURE); + } // print bloom filter details bloomrep.printBloomFilterDetails(); std::cout << "\n---------- reading and polishing draft : " << ctime(&rawtime); - readAndCorrect(bloom,bloomrep); + readAndCorrect(bloom, bloomrep); - } - else { + } else { std::cout << "---------- reading and polishing draft : " << ctime(&rawtime); - BloomFilter bloomrep(1000,1,1); - readAndCorrect(bloom,bloomrep); + BloomFilter bloomrep(1000, 1, 1); + readAndCorrect(bloom, bloomrep); } time(&rawtime); std::cout << "---------- process complete : " << ctime(&rawtime); From 46bbce654cf356f178080584af59d680f08fdc2b Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Fri, 3 Apr 2020 15:19:32 -0700 Subject: [PATCH 04/13] ntedit: clang-tidy Former-commit-id: 6a5ef928ccc61202ad74196b73ad2e6ab6ea806d --- ntedit.cpp | 282 +++++++++++++++++++++++------------------------------ 1 file changed, 122 insertions(+), 160 deletions(-) diff --git a/ntedit.cpp b/ntedit.cpp index 6258976..8144ad2 100644 --- a/ntedit.cpp +++ b/ntedit.cpp @@ -44,37 +44,31 @@ static const char USAGE_MESSAGE[] = PROGRAM " -t, number of threads [default=1]\n" " -f, draft genome assembly (FASTA, Multi-FASTA, and/or gzipped compatible), REQUIRED\n" " -r, Bloom filter file (generated from ntHits), REQUIRED\n" - " -e, secondary Bloom filter with kmers to reject (generated from ntHits), OPTIONAL. " - "EXPERIMENTAL\n" + " -e, secondary Bloom filter with kmers to reject (generated from ntHits), OPTIONAL. EXPERIMENTAL\n" " -b, output file prefix, OPTIONAL\n" " -z, minimum contig length [default=100]\n" " -i, maximum number of insertion bases to try, range 0-5, [default=4]\n" " -d, maximum number of deletions bases to try, range 0-5, [default=5]\n" " -x, k/x ratio for the number of kmers that should be missing, [default=5.000]\n" " -y, k/y ratio for the number of editted kmers that should be present, [default=9.000]\n" - " -X, ratio of number of kmers in the k subset that should be missing in order to " - "attempt fix (higher=stringent), [default=0.5]\n" - " -Y, ratio of number of kmers in the k subset that should be present to accept an edit " - "(higher=stringent), [default=0.5]\n" - " -c, cap for the number of base insertions that can be made at one position, " - "[default=k*1.5]\n" - " -j, controls size of kmer subset. When checking subset of kmers, check every jth kmer, " - "[default=3]\n" + " -X, ratio of number of kmers in the k subset that should be missing in order to attempt fix (higher=stringent), [default=0.5]\n" + " -Y, ratio of number of kmers in the k subset that should be present to accept an edit (higher=stringent), [default=0.5]\n" + " -c, cap for the number of base insertions that can be made at one position, [default=k*1.5]\n" + " -j, controls size of kmer subset. When checking subset of kmers, check every jth kmer, [default=3]\n" " -m, mode of editing, range 0-2, [default=0]\n" " 0: best substitution, or first good indel\n" " 1: best substitution, or best indel\n" " 2: best edit overall (suggestion that you reduce i and d for performance)\n" - " -s, SNV mode. Overrides draft kmer checks, forcing reassessment at each position (-s 1 " - "= yes, default = 0, no. EXPERIMENTAL)\n" + " -s, SNV mode. Overrides draft kmer checks, forcing reassessment at each position (-s 1 = yes, default = 0, no. EXPERIMENTAL)\n" " -v, verbose mode (-v 1 = yes, default = 0, no)\n" "\n" " --help, display this message and exit \n" " --version, output version information and exit\n" "\n" - " If one of X/Y is set, ntEdit will use those parameters instead. Otherwise, it uses x/y by " - "default.\n" + " If one of X/Y is set, ntEdit will use those parameters instead. Otherwise, it uses x/y by default.\n" "\n"; + namespace opt { /* Defining magical numbers. */ constexpr int default_min_contig_len = 100; @@ -88,10 +82,10 @@ float missing_ratio = 0.5; bool use_ratio = false; unsigned jump = 3; unsigned nthreads = 1; -std::string draft_filename; // NOLINT -std::string bloom_filename; // NOLINT +std::string draft_filename; // NOLINT +std::string bloom_filename; // NOLINT std::string bloomrep_filename; // NOLINT -std::string outfile_prefix; // NOLINT +std::string outfile_prefix; // NOLINT unsigned k; unsigned h = 0; unsigned e = 0; @@ -132,7 +126,7 @@ static const struct option longopts[] = { { "bloomrep_filename", required_argument, nullptr, 'e' }, { "outfile_prefix", required_argument, nullptr, 'b' }, { "mode", required_argument, nullptr, 'm' }, - { "snv", required_argument, nullptr, 's' }, + { "snv", required_argument, nullptr, 's' }, { "verbose", required_argument, nullptr, 'v' }, { "help", no_argument, nullptr, OPT_HELP }, { "version", no_argument, nullptr, OPT_VERSION }, @@ -757,9 +751,8 @@ writeEditsToFile( rfout << contigHdr.c_str() << "\t" << pos + 1 << "\t" << draft_char << "\t+" << insertion_bases.c_str() << "\t" << num_support << "\n"; - vfout << contigHdr.c_str() << "\t" << pos + 1 << "\t.\t" << draft_char << "\t" - << draft_char << insertion_bases.c_str() << "\t.\tPASS\tDP=" << num_support - << "\n"; + vfout << contigHdr.c_str() << "\t" << pos + 1 << "\t.\t" << draft_char << "\t" + << draft_char << insertion_bases.c_str() << "\t.\tPASS\tDP=" << num_support << "\n"; insertion_bases = ""; num_support = -1; @@ -772,27 +765,23 @@ writeEditsToFile( << substitution_record.front().sub_base << "\t" << substitution_record.front().num_support; std::string base(1, substitution_record.front().sub_base); - std::string support = ""; - support += std::to_string(substitution_record.front().num_support); - if (substitution_record.front().altsupp1 > 0) { // XXRLWXX - rfout << "\t" << substitution_record.front().altbase1 << "\t" - << substitution_record.front().altsupp1; + std::string support = std::to_string(substitution_record.front().num_support); + if (substitution_record.front().altsupp1 > 0){//XXRLWXX + rfout << "\t" << substitution_record.front().altbase1 << "\t" << substitution_record.front().altsupp1; base += ","; base += substitution_record.front().altbase1; support += ","; support += std::to_string(substitution_record.front().altsupp1); } - if (substitution_record.front().altsupp2 > 0) { // XXRLWXX - rfout << "\t" << substitution_record.front().altbase2 << "\t" - << substitution_record.front().altsupp2; + if (substitution_record.front().altsupp2 > 0){//XXRLWXX + rfout << "\t" << substitution_record.front().altbase2 << "\t" << substitution_record.front().altsupp2; base += ","; base += substitution_record.front().altbase2; support += ","; support += std::to_string(substitution_record.front().altsupp2); } - if (substitution_record.front().altsupp3 > 0) { // XXRLWXX - rfout << "\t" << substitution_record.front().altbase3 << "\t" - << substitution_record.front().altsupp3; + if (substitution_record.front().altsupp3 > 0){//XXRLWXX + rfout << "\t" << substitution_record.front().altbase3 << "\t" << substitution_record.front().altsupp3; base += ","; base += substitution_record.front().altbase3; support += ","; @@ -800,10 +789,9 @@ writeEditsToFile( } rfout << "\n"; - vfout << contigHdr.c_str() << "\t" << substitution_record.front().pos + 1 << "\t.\t" - << substitution_record.front().draft_char << "\t" << base - << "\t.\tPASS\tDP=" << support << "\n"; - + vfout << contigHdr.c_str() << "\t" << substitution_record.front().pos + 1 << "\t.\t" << substitution_record.front().draft_char << "\t" + << base << "\t.\tPASS\tDP=" << support << "\n"; + substitution_record.pop(); } // fprintf(dfout, "%s", contigSeq.substr(curr_node.s_pos, @@ -828,13 +816,14 @@ writeEditsToFile( << contigSeq.substr(pos, (curr_node.s_pos - pos)).c_str() << "\t" << curr_node.num_support << "\n"; - vfout << contigHdr.c_str() << "\t" << pos << "\t.\t" - << contigSeq.substr(pos - 1, (curr_node.s_pos - pos)).c_str() << "\t" - << contigSeq.at(pos - 1) << "\t.\tPASS\tDP=" << curr_node.num_support << "\n"; + vfout << contigHdr.c_str() << "\t" << pos << "\t.\t" << contigSeq.substr(pos-1, (curr_node.s_pos - pos)).c_str() << "\t" + << contigSeq.at(pos - 1) << "\t.\tPASS\tDP=" + << curr_node.num_support << "\n"; + } } } - dfout << "\n"; // FASTA RECORD + dfout << "\n";//FASTA RECORD } /* Roll ntHash using the seqNode structure. */ @@ -909,7 +898,7 @@ makeEdit( subst.num_support = best_num_support; if (altsupp1 && altbase1 != best_sub_base) { subst.altbase1 = altbase1; - subst.altsupp1 = altsupp1; + subst.altsupp1 = altsupp1; } if (altsupp2 && altbase2 != altbase1) { subst.altbase2 = altbase2; @@ -1096,8 +1085,7 @@ tryDeletion( charOut, charIn)) { NTMC64(charOut, charIn, opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); - if (k % opt::jump == 0 && bloom.contains(hVal) && - (!opt::secbf || !bloomrep.contains(hVal))) { + if (k%opt::jump == 0 && bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) { check_present++; } } @@ -1107,11 +1095,8 @@ tryDeletion( std::cout << "\t\tdeleting: " << deleted_bases << " check_present: " << check_present << std::endl; } - if ((!opt::use_ratio && - static_cast(check_present) >= (static_cast(opt::k) / opt::edit_threshold)) || - (opt::use_ratio && - static_cast(check_present) >= - (1 + (static_cast(opt::k) / opt::jump)) * opt::edit_ratio)) { // RLW + if ((!opt::use_ratio && static_cast(check_present) >= ( static_cast(opt::k) / opt::edit_threshold)) + || (opt::use_ratio && static_cast(check_present) >= ( 1 + ( static_cast(opt::k) / opt::jump )) * opt::edit_ratio)) { // RLW return static_cast(check_present); } return 0; @@ -1178,15 +1163,14 @@ tryIndels( for (; k < insertion_bases.size() - 1 && temp_h_seq_i < contigSeq.size(); k++) { NTMC64( getCharacter(temp_h_seq_i, newSeq[temp_h_node_index], contigSeq), - insertion_bases[k + 1], + insertion_bases[k+1], opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); increment(temp_h_seq_i, temp_h_node_index, newSeq); - if (k % opt::jump == 0 && bloom.contains(hVal) && - (!opt::secbf || !bloomrep.contains(hVal))) { // RLW + if (k % opt::jump == 0 && bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) {// RLW check_present++; } } @@ -1202,8 +1186,7 @@ tryIndels( charOut, charIn)) { NTMC64(charOut, charIn, opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); - if (k % opt::jump == 0 && bloom.contains(hVal) && - (!opt::secbf || !bloomrep.contains(hVal))) { // RLW + if (k % opt::jump == 0 && bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) {//RLW check_present++; } } @@ -1214,11 +1197,7 @@ tryIndels( << std::endl; } // if the insertion is good, store the insertion accordingly RLW - if ((!opt::use_ratio && static_cast(check_present) >= - (static_cast(opt::k) / opt::edit_threshold)) || - (opt::use_ratio && - static_cast(check_present) >= - (static_cast(opt::k) / opt::jump) * opt::edit_ratio)) { // RLW + if ((!opt::use_ratio && static_cast(check_present) >= (static_cast(opt::k) / opt::edit_threshold)) || (opt::use_ratio && static_cast(check_present) >= ( static_cast(opt::k) / opt::jump) * opt::edit_ratio)) { // RLW if (opt::mode == 0) { // if we are in default mode, we just accept this first good insertion and return best_edit_type = 2; @@ -1229,7 +1208,7 @@ tryIndels( if (opt::mode == 1 || opt::mode == 2) { // if we are in some deep mode, we look for the best indel within index char first if (check_present >= temp_best_num_support) { - if (temp_best_num_support) { + if(temp_best_num_support) { temp_alt_indel = temp_best_indel; temp_alt_num_support = temp_best_num_support; } @@ -1266,7 +1245,7 @@ tryIndels( } if (opt::mode == 1 || opt::mode == 2) { if (del_support >= temp_best_num_support) { - if (temp_best_num_support) { + if(temp_best_num_support) { temp_alt_indel = temp_best_indel; temp_alt_num_support = temp_best_num_support; } @@ -1369,8 +1348,7 @@ kmerizeAndCorrect( unsigned check_missing = 0; unsigned check_there = 0; // RLW bool do_not_fix = false; - for (unsigned k = 0; k < opt::k && temp_h_seq_i < seqLen; - k++) { // RLW -- below roll may be adjusted/dupli to account for gapped seed + for (unsigned k = 0; k < opt::k && temp_h_seq_i < seqLen; k++) { // RLW -- below roll may be adjusted/dupli to account for gapped seed if (roll( temp_h_seq_i, temp_t_seq_i, @@ -1387,7 +1365,8 @@ kmerizeAndCorrect( } if (k % opt::jump == 0 && !bloom.contains(hVal)) { // RLW check_missing++; - } else if (k % opt::jump == 0 && bloom.contains(hVal)) { // XXRLWXX + } + else if(k % opt::jump == 0 && bloom.contains(hVal)){ // XXRLWXX check_there++; } } else { @@ -1399,13 +1378,8 @@ kmerizeAndCorrect( if (opt::verbose) { std::cout << "\tcheck_missing: " << check_missing << std::endl; } - if ((opt::snv) || ((!do_not_fix) && - (((!opt::use_ratio && - static_cast(check_missing) >= - (static_cast(opt::k) / opt::missing_threshold))) || - ((opt::use_ratio && static_cast(check_missing) >= - ((static_cast(opt::k) / opt::jump) * - opt::missing_ratio)))))) { // RLW + if ((opt::snv) || ((!do_not_fix) && (((!opt::use_ratio && static_cast(check_missing) >= (static_cast(opt::k) / opt::missing_threshold))) + || ((opt::use_ratio && static_cast(check_missing) >= (( static_cast(opt::k) / opt::jump) * opt::missing_ratio)))))) { // RLW // recorders unsigned num_deletions = 1; @@ -1418,27 +1392,23 @@ kmerizeAndCorrect( unsigned char altbase1; unsigned char altbase2; unsigned char altbase3; - unsigned altsupp1 = 0; + unsigned altsupp1 = 0; unsigned altsupp2 = 0; unsigned altsupp3 = 0; - if (opt::snv) { // XXRLWXX -- sets baseline for draft + if(opt::snv){ // XXRLWXX -- sets baseline for draft - if ((!opt::use_ratio && - static_cast(check_there) >= - (static_cast(opt::k) / opt::edit_threshold)) || - (opt::use_ratio && - static_cast(check_there) >= - ((static_cast(opt::k) / opt::jump)) * opt::edit_ratio)) { + if ((!opt::use_ratio && static_cast(check_there) >= (static_cast(opt::k) / opt::edit_threshold)) + || (opt::use_ratio && static_cast(check_there) >= (( static_cast(opt::k) / opt::jump))*opt::edit_ratio)) { best_sub_base = draft_char; best_num_support = check_there; if (opt::verbose) { std::cout << "\t\tORI BEST SUB BASE: " << best_sub_base - << " NUMBER: " << best_num_support << std::endl; + << " NUMBER: " << best_num_support << std::endl; } } - } + } // try substitution for (const unsigned char sub_base : bases_array[draft_char]) { @@ -1451,8 +1421,7 @@ kmerizeAndCorrect( draft_char, sub_base, opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); // only do verification of substitution if it is found in Bloom filter - if ((bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) || - opt::mode == 2) { + if ((bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) || opt::mode == 2) { // reset temporary values temp_h_node_index = h_node_index; temp_t_node_index = t_node_index; @@ -1481,8 +1450,7 @@ kmerizeAndCorrect( charIn)) { NTMC64( charOut, charIn, opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); - if (k % opt::jump == 0 && bloom.contains(hVal) && - (!opt::secbf || !bloomrep.contains(hVal))) { // RLW + if (k % opt::jump == 0 && bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) { // RLW check_present++; } } else { @@ -1501,12 +1469,8 @@ kmerizeAndCorrect( << " check_present: " << check_present << std::endl; } - if ((!opt::use_ratio && - static_cast(check_present) >= - (static_cast(opt::k) / opt::edit_threshold)) || - (opt::use_ratio && static_cast(check_present) >= - ((static_cast(opt::k) / opt::jump)) * - opt::edit_ratio)) { // RLW + if ((!opt::use_ratio && static_cast(check_present) >= (static_cast(opt::k) / opt::edit_threshold)) + || (opt::use_ratio && static_cast(check_present) >= (( static_cast(opt::k) / opt::jump))*opt::edit_ratio)) { // RLW // update the best substitution if (check_present >= best_num_support) { @@ -1514,22 +1478,22 @@ kmerizeAndCorrect( altbase3 = altbase2; altsupp3 = altsupp2; } - if (altsupp1) { + if(altsupp1) { altbase2 = altbase1; altsupp2 = altsupp1; } - if (best_num_support) { + if(best_num_support) { altsupp1 = best_num_support; altbase1 = best_sub_base; } best_edit_type = 1; best_sub_base = sub_base; best_num_support = check_present; - } else { - if (!altsupp1) { + } else{ + if (! altsupp1) { altbase1 = sub_base; altsupp1 = check_present; - } else if (!altsupp2) { + } else if (! altsupp2) { if (check_present < altsupp1) { altbase2 = sub_base; altsupp2 = check_present; @@ -1539,7 +1503,7 @@ kmerizeAndCorrect( altbase1 = sub_base; altsupp1 = check_present; } - } else if (!altsupp3) { + } else if (! altsupp3) { if (check_present < altsupp2) { altbase3 = sub_base; altsupp3 = check_present; @@ -1581,7 +1545,7 @@ kmerizeAndCorrect( contigSeq, newSeq, bloom, - bloomrep, + bloomrep, best_edit_type, best_indel, alt_indel, @@ -1673,33 +1637,35 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) ofstream vfout; dfout.open(d_filename); rfout.open(r_filename); - // printf ( "OUT OF %.1f\n", ceil( double(opt::k) / double(opt::jump) ) ); + //printf ( "OUT OF %.1f\n", ceil( double(opt::k) / double(opt::jump) ) ); rfout << "ID\tbpPosition+1\tOriginalBase\tNewBase\tSupport " << opt::k << "-mer (out of " - << ceil(double(opt::k) / double(opt::jump)) << ")\tAlt.Base1\tAlt.Support1\t" + << ceil( double(opt::k) / double(opt::jump)) << ")\tAlt.Base1\tAlt.Support1\t" << "Alt.Base2\tAlt.Support2\tAlt.Base3\tAlt.Support3\n"; // RLW - vfout.open(v_filename); - - vfout << "##fileformat=VCFv4.2" << std::endl; - time_t now = time(0); - tm* ltm = localtime(&now); - std::string year = std::to_string(1900 + ltm->tm_year); - std::string month = std::to_string(1 + ltm->tm_mon); - if (month.size() < 2) { - month.insert(0, "0"); - } - std::string day = std::to_string(ltm->tm_mday); - if (day.size() < 2) { - day.insert(0, "0"); - } + vfout.open(v_filename); + + vfout << "##fileformat=VCFv4.2" << std::endl; + + time_t now = time(nullptr); + tm *ltm = localtime(&now); + std::string year = std::to_string(1900 + ltm->tm_year); + std::string month = std::to_string(1 + ltm->tm_mon); + if (month.size() < 2) { + month.insert(0, "0"); + } + std::string day = std::to_string(ltm->tm_mday); + if (day.size() < 2) { + day.insert(0, "0"); + } + + vfout << "##fileDate=" << year << month << day << std::endl; + vfout << "##source=ntEditV1.3.2" << std::endl; + vfout << "##reference=file:" << opt::draft_filename <" << std::endl; + vfout << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" << std::endl; - vfout << "##fileDate=" << year << month << day << std::endl; - vfout << "##source=ntEditV1.3.2" << std::endl; - vfout << "##reference=file:" << opt::draft_filename << std::endl; - vfout << "##FORMAT=" << std::endl; - vfout << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" << std::endl; #pragma omp parallel shared(seq, dfout, rfout, vfout) { @@ -1731,8 +1697,7 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) std::cout << contigName << std::endl; } if (seq_len >= opt::min_contig_len) { - kmerizeAndCorrect( - contigName, contigSeq, seq_len, bloom, bloomrep, dfout, rfout, vfout); + kmerizeAndCorrect(contigName, contigSeq, seq_len, bloom, bloomrep, dfout, rfout, vfout); } #pragma omp atomic num_contigs++; @@ -1746,7 +1711,7 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) gzclose(dfp); dfout.close(); rfout.close(); - vfout.close(); + vfout.close(); } int @@ -1791,11 +1756,11 @@ main(int argc, char** argv) break; case 'X': arg >> opt::missing_ratio; - opt::use_ratio = true; + opt::use_ratio=true; break; case 'Y': arg >> opt::edit_ratio; - opt::use_ratio = true; + opt::use_ratio=true; break; case 'c': arg >> opt::insertion_cap; @@ -1853,7 +1818,7 @@ main(int argc, char** argv) // check that the repeat bloom filter file is specified - RLW2019 if (opt::bloomrep_filename.empty()) { - opt::secbf = 0; // flag will track whether to query secondary Bloom filter or not + opt::secbf = 0;//flag will track whether to query secondary Bloom filter or not } else { // if the file is specified check that it is readable opt::secbf = 1; @@ -1866,11 +1831,10 @@ main(int argc, char** argv) } // added nov21 2019 XXRLW - if (opt::snv) { + if(opt::snv){ opt::max_insertions = 0; opt::max_deletions = 0; - std::cerr << PROGRAM ": EXPERIMENTAL feature note: i and d set to 0 when s is set to 1; " - "Only tracking single-base variants.\n"; + std::cerr << PROGRAM ": EXPERIMENTAL feature note: i and d set to 0 when s is set to 1; Only tracking single-base variants.\n"; } // get the basename for the file @@ -1886,8 +1850,7 @@ main(int argc, char** argv) // Load bloom filter time(&rawtime); - std::cout << "---------- loading Bloom filter from file : " << ctime(&rawtime) - << "\n"; + std::cout << "---------- loading Bloom filter from file : " << ctime(&rawtime) << "\n"; BloomFilter bloom(opt::bloom_filename.c_str()); opt::h = bloom.getHashNum(); @@ -1900,14 +1863,13 @@ main(int argc, char** argv) // assign k from Bloom filter header opt::k = bloom.getKmerSize(); - opt::insertion_cap = - static_cast(static_cast(opt::k) * opt::default_insertion_cap_ratio); + opt::insertion_cap = static_cast(static_cast(opt::k) * opt::default_insertion_cap_ratio); // print bloom filter details bloom.printBloomFilterDetails(); // Checking parameters - time(&rawtime); + time(&rawtime); std::cout << "\n---------- verifying parameters : " << ctime(&rawtime); // check that the parameters x and y are in bound if (opt::missing_threshold < 3 && opt::missing_threshold > static_cast(opt::k) && @@ -1938,10 +1900,10 @@ main(int argc, char** argv) } // print parameters: - std::cout << "\nrunning : " << PROGRAM << "\n -f " << draft_basename << "\n -k " << opt::k - << "\n -z " << opt::min_contig_len << "\n -b " << opt::outfile_prefix << "\n -r " - << bloom_basename << "\n -e " << bloomrep_basename << "\n -i " << opt::max_insertions - << "\n -d " << opt::max_deletions; + std::cout << "\nrunning : " << PROGRAM << "\n -f " << draft_basename + << "\n -k " << opt::k << "\n -z " << opt::min_contig_len << "\n -b " + << opt::outfile_prefix << "\n -r " << bloom_basename << "\n -e " << bloomrep_basename + << "\n -i " << opt::max_insertions << "\n -d " << opt::max_deletions; if (opt::use_ratio) { // RLW std::cout << "\n -X " << opt::missing_ratio << "\n -Y " << opt::edit_ratio; @@ -1949,43 +1911,43 @@ main(int argc, char** argv) std::cout << "\n -x " << opt::missing_threshold << "\n -y " << opt::edit_threshold; } - std::cout << "\n -j " << opt::jump << "\n -m " << opt::mode << "\n -s " << opt::snv << "\n -t " - << opt::nthreads << "\n -v " << opt::verbose << "\n" - << std::endl; + std::cout << "\n -j " << opt::jump << "\n -m " << opt::mode + << "\n -s " << opt::snv << "\n -t " << opt::nthreads << "\n -v " << opt::verbose << "\n" << std::endl; // Read & edit contigs time(&rawtime); if (opt::secbf) { time(&rawtime); - std::cout << "---------- loading secondary Bloom filter from file : " << ctime(&rawtime) - << "\n"; - BloomFilter bloomrep(opt::bloomrep_filename.c_str()); - opt::e = bloomrep.getHashNum(); - - // Checks for the Bloom filter - if (opt::e == 0) { - std::cerr << PROGRAM - ": error: secondary Bloom filter file supplied (-e) is incorrect.\n"; - exit(EXIT_FAILURE); - } + std::cout << "---------- loading secondary Bloom filter from file : " << ctime(&rawtime) << "\n"; + BloomFilter bloomrep(opt::bloomrep_filename.c_str()); + opt::e = bloomrep.getHashNum(); + + // Checks for the Bloom filter + if (opt::e == 0) { + std::cerr << PROGRAM ": error: secondary Bloom filter file supplied (-e) is incorrect.\n"; + exit(EXIT_FAILURE); + } // Check that primary and secondary BF kmer sizes match - if (opt::k != bloomrep.getKmerSize()) { - std::cerr << PROGRAM ": error: secondary Bloom filter k size (" - << bloomrep.getKmerSize() << ") is different than main Bloom filter k size (" - << opt::k << ")\n"; - exit(EXIT_FAILURE); - } + if (opt::k != bloomrep.getKmerSize()) { + std::cerr << PROGRAM ": error: secondary Bloom filter k size (" + << bloomrep.getKmerSize() + << ") is different than main Bloom filter k size (" + << opt::k + << ")\n"; + exit(EXIT_FAILURE); + } // print bloom filter details bloomrep.printBloomFilterDetails(); std::cout << "\n---------- reading and polishing draft : " << ctime(&rawtime); - readAndCorrect(bloom, bloomrep); + readAndCorrect(bloom,bloomrep); - } else { + } + else { std::cout << "---------- reading and polishing draft : " << ctime(&rawtime); - BloomFilter bloomrep(1000, 1, 1); - readAndCorrect(bloom, bloomrep); + BloomFilter bloomrep(1000,1,1); + readAndCorrect(bloom,bloomrep); } time(&rawtime); std::cout << "---------- process complete : " << ctime(&rawtime); From 6a3e48a3a7181d94273b389fe6172262f3178fb8 Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Fri, 3 Apr 2020 15:40:54 -0700 Subject: [PATCH 05/13] ntedit: fix deletion bug in vcf Former-commit-id: c8a9fe5fe7df357b6d6f46fa88911f35cb1ece49 --- ntedit.cpp | 279 ++++++++++++++++++++++++++++++----------------------- 1 file changed, 158 insertions(+), 121 deletions(-) diff --git a/ntedit.cpp b/ntedit.cpp index 8144ad2..8dc31ee 100644 --- a/ntedit.cpp +++ b/ntedit.cpp @@ -44,31 +44,37 @@ static const char USAGE_MESSAGE[] = PROGRAM " -t, number of threads [default=1]\n" " -f, draft genome assembly (FASTA, Multi-FASTA, and/or gzipped compatible), REQUIRED\n" " -r, Bloom filter file (generated from ntHits), REQUIRED\n" - " -e, secondary Bloom filter with kmers to reject (generated from ntHits), OPTIONAL. EXPERIMENTAL\n" + " -e, secondary Bloom filter with kmers to reject (generated from ntHits), OPTIONAL. " + "EXPERIMENTAL\n" " -b, output file prefix, OPTIONAL\n" " -z, minimum contig length [default=100]\n" " -i, maximum number of insertion bases to try, range 0-5, [default=4]\n" " -d, maximum number of deletions bases to try, range 0-5, [default=5]\n" " -x, k/x ratio for the number of kmers that should be missing, [default=5.000]\n" " -y, k/y ratio for the number of editted kmers that should be present, [default=9.000]\n" - " -X, ratio of number of kmers in the k subset that should be missing in order to attempt fix (higher=stringent), [default=0.5]\n" - " -Y, ratio of number of kmers in the k subset that should be present to accept an edit (higher=stringent), [default=0.5]\n" - " -c, cap for the number of base insertions that can be made at one position, [default=k*1.5]\n" - " -j, controls size of kmer subset. When checking subset of kmers, check every jth kmer, [default=3]\n" + " -X, ratio of number of kmers in the k subset that should be missing in order to " + "attempt fix (higher=stringent), [default=0.5]\n" + " -Y, ratio of number of kmers in the k subset that should be present to accept an edit " + "(higher=stringent), [default=0.5]\n" + " -c, cap for the number of base insertions that can be made at one position, " + "[default=k*1.5]\n" + " -j, controls size of kmer subset. When checking subset of kmers, check every jth kmer, " + "[default=3]\n" " -m, mode of editing, range 0-2, [default=0]\n" " 0: best substitution, or first good indel\n" " 1: best substitution, or best indel\n" " 2: best edit overall (suggestion that you reduce i and d for performance)\n" - " -s, SNV mode. Overrides draft kmer checks, forcing reassessment at each position (-s 1 = yes, default = 0, no. EXPERIMENTAL)\n" + " -s, SNV mode. Overrides draft kmer checks, forcing reassessment at each position (-s 1 " + "= yes, default = 0, no. EXPERIMENTAL)\n" " -v, verbose mode (-v 1 = yes, default = 0, no)\n" "\n" " --help, display this message and exit \n" " --version, output version information and exit\n" "\n" - " If one of X/Y is set, ntEdit will use those parameters instead. Otherwise, it uses x/y by default.\n" + " If one of X/Y is set, ntEdit will use those parameters instead. Otherwise, it uses x/y by " + "default.\n" "\n"; - namespace opt { /* Defining magical numbers. */ constexpr int default_min_contig_len = 100; @@ -82,10 +88,10 @@ float missing_ratio = 0.5; bool use_ratio = false; unsigned jump = 3; unsigned nthreads = 1; -std::string draft_filename; // NOLINT -std::string bloom_filename; // NOLINT +std::string draft_filename; // NOLINT +std::string bloom_filename; // NOLINT std::string bloomrep_filename; // NOLINT -std::string outfile_prefix; // NOLINT +std::string outfile_prefix; // NOLINT unsigned k; unsigned h = 0; unsigned e = 0; @@ -126,7 +132,7 @@ static const struct option longopts[] = { { "bloomrep_filename", required_argument, nullptr, 'e' }, { "outfile_prefix", required_argument, nullptr, 'b' }, { "mode", required_argument, nullptr, 'm' }, - { "snv", required_argument, nullptr, 's' }, + { "snv", required_argument, nullptr, 's' }, { "verbose", required_argument, nullptr, 'v' }, { "help", no_argument, nullptr, OPT_HELP }, { "version", no_argument, nullptr, OPT_VERSION }, @@ -751,8 +757,9 @@ writeEditsToFile( rfout << contigHdr.c_str() << "\t" << pos + 1 << "\t" << draft_char << "\t+" << insertion_bases.c_str() << "\t" << num_support << "\n"; - vfout << contigHdr.c_str() << "\t" << pos + 1 << "\t.\t" << draft_char << "\t" - << draft_char << insertion_bases.c_str() << "\t.\tPASS\tDP=" << num_support << "\n"; + vfout << contigHdr.c_str() << "\t" << pos + 1 << "\t.\t" << draft_char << "\t" + << draft_char << insertion_bases.c_str() << "\t.\tPASS\tDP=" << num_support + << "\n"; insertion_bases = ""; num_support = -1; @@ -766,22 +773,25 @@ writeEditsToFile( << substitution_record.front().num_support; std::string base(1, substitution_record.front().sub_base); std::string support = std::to_string(substitution_record.front().num_support); - if (substitution_record.front().altsupp1 > 0){//XXRLWXX - rfout << "\t" << substitution_record.front().altbase1 << "\t" << substitution_record.front().altsupp1; + if (substitution_record.front().altsupp1 > 0) { // XXRLWXX + rfout << "\t" << substitution_record.front().altbase1 << "\t" + << substitution_record.front().altsupp1; base += ","; base += substitution_record.front().altbase1; support += ","; support += std::to_string(substitution_record.front().altsupp1); } - if (substitution_record.front().altsupp2 > 0){//XXRLWXX - rfout << "\t" << substitution_record.front().altbase2 << "\t" << substitution_record.front().altsupp2; + if (substitution_record.front().altsupp2 > 0) { // XXRLWXX + rfout << "\t" << substitution_record.front().altbase2 << "\t" + << substitution_record.front().altsupp2; base += ","; base += substitution_record.front().altbase2; support += ","; support += std::to_string(substitution_record.front().altsupp2); } - if (substitution_record.front().altsupp3 > 0){//XXRLWXX - rfout << "\t" << substitution_record.front().altbase3 << "\t" << substitution_record.front().altsupp3; + if (substitution_record.front().altsupp3 > 0) { // XXRLWXX + rfout << "\t" << substitution_record.front().altbase3 << "\t" + << substitution_record.front().altsupp3; base += ","; base += substitution_record.front().altbase3; support += ","; @@ -789,9 +799,10 @@ writeEditsToFile( } rfout << "\n"; - vfout << contigHdr.c_str() << "\t" << substitution_record.front().pos + 1 << "\t.\t" << substitution_record.front().draft_char << "\t" - << base << "\t.\tPASS\tDP=" << support << "\n"; - + vfout << contigHdr.c_str() << "\t" << substitution_record.front().pos + 1 << "\t.\t" + << substitution_record.front().draft_char << "\t" << base + << "\t.\tPASS\tDP=" << support << "\n"; + substitution_record.pop(); } // fprintf(dfout, "%s", contigSeq.substr(curr_node.s_pos, @@ -816,14 +827,13 @@ writeEditsToFile( << contigSeq.substr(pos, (curr_node.s_pos - pos)).c_str() << "\t" << curr_node.num_support << "\n"; - vfout << contigHdr.c_str() << "\t" << pos << "\t.\t" << contigSeq.substr(pos-1, (curr_node.s_pos - pos)).c_str() << "\t" - << contigSeq.at(pos - 1) << "\t.\tPASS\tDP=" - << curr_node.num_support << "\n"; - + vfout << contigHdr.c_str() << "\t" << pos << "\t.\t" + << contigSeq.substr(pos - 1, (curr_node.s_pos - pos) + 1).c_str() << "\t" + << contigSeq.at(pos - 1) << "\t.\tPASS\tDP=" << curr_node.num_support << "\n"; } } } - dfout << "\n";//FASTA RECORD + dfout << "\n"; // FASTA RECORD } /* Roll ntHash using the seqNode structure. */ @@ -898,7 +908,7 @@ makeEdit( subst.num_support = best_num_support; if (altsupp1 && altbase1 != best_sub_base) { subst.altbase1 = altbase1; - subst.altsupp1 = altsupp1; + subst.altsupp1 = altsupp1; } if (altsupp2 && altbase2 != altbase1) { subst.altbase2 = altbase2; @@ -1085,7 +1095,8 @@ tryDeletion( charOut, charIn)) { NTMC64(charOut, charIn, opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); - if (k%opt::jump == 0 && bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) { + if (k % opt::jump == 0 && bloom.contains(hVal) && + (!opt::secbf || !bloomrep.contains(hVal))) { check_present++; } } @@ -1095,8 +1106,11 @@ tryDeletion( std::cout << "\t\tdeleting: " << deleted_bases << " check_present: " << check_present << std::endl; } - if ((!opt::use_ratio && static_cast(check_present) >= ( static_cast(opt::k) / opt::edit_threshold)) - || (opt::use_ratio && static_cast(check_present) >= ( 1 + ( static_cast(opt::k) / opt::jump )) * opt::edit_ratio)) { // RLW + if ((!opt::use_ratio && + static_cast(check_present) >= (static_cast(opt::k) / opt::edit_threshold)) || + (opt::use_ratio && + static_cast(check_present) >= + (1 + (static_cast(opt::k) / opt::jump)) * opt::edit_ratio)) { // RLW return static_cast(check_present); } return 0; @@ -1163,14 +1177,15 @@ tryIndels( for (; k < insertion_bases.size() - 1 && temp_h_seq_i < contigSeq.size(); k++) { NTMC64( getCharacter(temp_h_seq_i, newSeq[temp_h_node_index], contigSeq), - insertion_bases[k+1], + insertion_bases[k + 1], opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); increment(temp_h_seq_i, temp_h_node_index, newSeq); - if (k % opt::jump == 0 && bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) {// RLW + if (k % opt::jump == 0 && bloom.contains(hVal) && + (!opt::secbf || !bloomrep.contains(hVal))) { // RLW check_present++; } } @@ -1186,7 +1201,8 @@ tryIndels( charOut, charIn)) { NTMC64(charOut, charIn, opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); - if (k % opt::jump == 0 && bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) {//RLW + if (k % opt::jump == 0 && bloom.contains(hVal) && + (!opt::secbf || !bloomrep.contains(hVal))) { // RLW check_present++; } } @@ -1197,7 +1213,11 @@ tryIndels( << std::endl; } // if the insertion is good, store the insertion accordingly RLW - if ((!opt::use_ratio && static_cast(check_present) >= (static_cast(opt::k) / opt::edit_threshold)) || (opt::use_ratio && static_cast(check_present) >= ( static_cast(opt::k) / opt::jump) * opt::edit_ratio)) { // RLW + if ((!opt::use_ratio && static_cast(check_present) >= + (static_cast(opt::k) / opt::edit_threshold)) || + (opt::use_ratio && + static_cast(check_present) >= + (static_cast(opt::k) / opt::jump) * opt::edit_ratio)) { // RLW if (opt::mode == 0) { // if we are in default mode, we just accept this first good insertion and return best_edit_type = 2; @@ -1208,7 +1228,7 @@ tryIndels( if (opt::mode == 1 || opt::mode == 2) { // if we are in some deep mode, we look for the best indel within index char first if (check_present >= temp_best_num_support) { - if(temp_best_num_support) { + if (temp_best_num_support) { temp_alt_indel = temp_best_indel; temp_alt_num_support = temp_best_num_support; } @@ -1245,7 +1265,7 @@ tryIndels( } if (opt::mode == 1 || opt::mode == 2) { if (del_support >= temp_best_num_support) { - if(temp_best_num_support) { + if (temp_best_num_support) { temp_alt_indel = temp_best_indel; temp_alt_num_support = temp_best_num_support; } @@ -1348,7 +1368,8 @@ kmerizeAndCorrect( unsigned check_missing = 0; unsigned check_there = 0; // RLW bool do_not_fix = false; - for (unsigned k = 0; k < opt::k && temp_h_seq_i < seqLen; k++) { // RLW -- below roll may be adjusted/dupli to account for gapped seed + for (unsigned k = 0; k < opt::k && temp_h_seq_i < seqLen; + k++) { // RLW -- below roll may be adjusted/dupli to account for gapped seed if (roll( temp_h_seq_i, temp_t_seq_i, @@ -1365,8 +1386,7 @@ kmerizeAndCorrect( } if (k % opt::jump == 0 && !bloom.contains(hVal)) { // RLW check_missing++; - } - else if(k % opt::jump == 0 && bloom.contains(hVal)){ // XXRLWXX + } else if (k % opt::jump == 0 && bloom.contains(hVal)) { // XXRLWXX check_there++; } } else { @@ -1378,8 +1398,13 @@ kmerizeAndCorrect( if (opt::verbose) { std::cout << "\tcheck_missing: " << check_missing << std::endl; } - if ((opt::snv) || ((!do_not_fix) && (((!opt::use_ratio && static_cast(check_missing) >= (static_cast(opt::k) / opt::missing_threshold))) - || ((opt::use_ratio && static_cast(check_missing) >= (( static_cast(opt::k) / opt::jump) * opt::missing_ratio)))))) { // RLW + if ((opt::snv) || ((!do_not_fix) && + (((!opt::use_ratio && + static_cast(check_missing) >= + (static_cast(opt::k) / opt::missing_threshold))) || + ((opt::use_ratio && static_cast(check_missing) >= + ((static_cast(opt::k) / opt::jump) * + opt::missing_ratio)))))) { // RLW // recorders unsigned num_deletions = 1; @@ -1392,23 +1417,27 @@ kmerizeAndCorrect( unsigned char altbase1; unsigned char altbase2; unsigned char altbase3; - unsigned altsupp1 = 0; + unsigned altsupp1 = 0; unsigned altsupp2 = 0; unsigned altsupp3 = 0; - if(opt::snv){ // XXRLWXX -- sets baseline for draft + if (opt::snv) { // XXRLWXX -- sets baseline for draft - if ((!opt::use_ratio && static_cast(check_there) >= (static_cast(opt::k) / opt::edit_threshold)) - || (opt::use_ratio && static_cast(check_there) >= (( static_cast(opt::k) / opt::jump))*opt::edit_ratio)) { + if ((!opt::use_ratio && + static_cast(check_there) >= + (static_cast(opt::k) / opt::edit_threshold)) || + (opt::use_ratio && + static_cast(check_there) >= + ((static_cast(opt::k) / opt::jump)) * opt::edit_ratio)) { best_sub_base = draft_char; best_num_support = check_there; if (opt::verbose) { std::cout << "\t\tORI BEST SUB BASE: " << best_sub_base - << " NUMBER: " << best_num_support << std::endl; + << " NUMBER: " << best_num_support << std::endl; } } - } + } // try substitution for (const unsigned char sub_base : bases_array[draft_char]) { @@ -1421,7 +1450,8 @@ kmerizeAndCorrect( draft_char, sub_base, opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); // only do verification of substitution if it is found in Bloom filter - if ((bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) || opt::mode == 2) { + if ((bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) || + opt::mode == 2) { // reset temporary values temp_h_node_index = h_node_index; temp_t_node_index = t_node_index; @@ -1450,7 +1480,8 @@ kmerizeAndCorrect( charIn)) { NTMC64( charOut, charIn, opt::k, opt::h, temp_fhVal, temp_rhVal, hVal); - if (k % opt::jump == 0 && bloom.contains(hVal) && (!opt::secbf || !bloomrep.contains(hVal))) { // RLW + if (k % opt::jump == 0 && bloom.contains(hVal) && + (!opt::secbf || !bloomrep.contains(hVal))) { // RLW check_present++; } } else { @@ -1469,8 +1500,12 @@ kmerizeAndCorrect( << " check_present: " << check_present << std::endl; } - if ((!opt::use_ratio && static_cast(check_present) >= (static_cast(opt::k) / opt::edit_threshold)) - || (opt::use_ratio && static_cast(check_present) >= (( static_cast(opt::k) / opt::jump))*opt::edit_ratio)) { // RLW + if ((!opt::use_ratio && + static_cast(check_present) >= + (static_cast(opt::k) / opt::edit_threshold)) || + (opt::use_ratio && static_cast(check_present) >= + ((static_cast(opt::k) / opt::jump)) * + opt::edit_ratio)) { // RLW // update the best substitution if (check_present >= best_num_support) { @@ -1478,22 +1513,22 @@ kmerizeAndCorrect( altbase3 = altbase2; altsupp3 = altsupp2; } - if(altsupp1) { + if (altsupp1) { altbase2 = altbase1; altsupp2 = altsupp1; } - if(best_num_support) { + if (best_num_support) { altsupp1 = best_num_support; altbase1 = best_sub_base; } best_edit_type = 1; best_sub_base = sub_base; best_num_support = check_present; - } else{ - if (! altsupp1) { + } else { + if (!altsupp1) { altbase1 = sub_base; altsupp1 = check_present; - } else if (! altsupp2) { + } else if (!altsupp2) { if (check_present < altsupp1) { altbase2 = sub_base; altsupp2 = check_present; @@ -1503,7 +1538,7 @@ kmerizeAndCorrect( altbase1 = sub_base; altsupp1 = check_present; } - } else if (! altsupp3) { + } else if (!altsupp3) { if (check_present < altsupp2) { altbase3 = sub_base; altsupp3 = check_present; @@ -1545,7 +1580,7 @@ kmerizeAndCorrect( contigSeq, newSeq, bloom, - bloomrep, + bloomrep, best_edit_type, best_indel, alt_indel, @@ -1637,35 +1672,33 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) ofstream vfout; dfout.open(d_filename); rfout.open(r_filename); - //printf ( "OUT OF %.1f\n", ceil( double(opt::k) / double(opt::jump) ) ); + // printf ( "OUT OF %.1f\n", ceil( double(opt::k) / double(opt::jump) ) ); rfout << "ID\tbpPosition+1\tOriginalBase\tNewBase\tSupport " << opt::k << "-mer (out of " - << ceil( double(opt::k) / double(opt::jump)) << ")\tAlt.Base1\tAlt.Support1\t" + << ceil(double(opt::k) / double(opt::jump)) << ")\tAlt.Base1\tAlt.Support1\t" << "Alt.Base2\tAlt.Support2\tAlt.Base3\tAlt.Support3\n"; // RLW + vfout.open(v_filename); + + vfout << "##fileformat=VCFv4.2" << std::endl; - vfout.open(v_filename); - - vfout << "##fileformat=VCFv4.2" << std::endl; - - time_t now = time(nullptr); - tm *ltm = localtime(&now); - std::string year = std::to_string(1900 + ltm->tm_year); - std::string month = std::to_string(1 + ltm->tm_mon); - if (month.size() < 2) { - month.insert(0, "0"); - } - std::string day = std::to_string(ltm->tm_mday); - if (day.size() < 2) { - day.insert(0, "0"); - } - - vfout << "##fileDate=" << year << month << day << std::endl; - vfout << "##source=ntEditV1.3.2" << std::endl; - vfout << "##reference=file:" << opt::draft_filename <" << std::endl; - vfout << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" << std::endl; + time_t now = time(nullptr); + tm* ltm = localtime(&now); + std::string year = std::to_string(1900 + ltm->tm_year); + std::string month = std::to_string(1 + ltm->tm_mon); + if (month.size() < 2) { + month.insert(0, "0"); + } + std::string day = std::to_string(ltm->tm_mday); + if (day.size() < 2) { + day.insert(0, "0"); + } + vfout << "##fileDate=" << year << month << day << std::endl; + vfout << "##source=ntEditV1.3.2" << std::endl; + vfout << "##reference=file:" << opt::draft_filename << std::endl; + vfout << "##INFO=" << std::endl; + vfout << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" << std::endl; #pragma omp parallel shared(seq, dfout, rfout, vfout) { @@ -1697,7 +1730,8 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) std::cout << contigName << std::endl; } if (seq_len >= opt::min_contig_len) { - kmerizeAndCorrect(contigName, contigSeq, seq_len, bloom, bloomrep, dfout, rfout, vfout); + kmerizeAndCorrect( + contigName, contigSeq, seq_len, bloom, bloomrep, dfout, rfout, vfout); } #pragma omp atomic num_contigs++; @@ -1711,7 +1745,7 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) gzclose(dfp); dfout.close(); rfout.close(); - vfout.close(); + vfout.close(); } int @@ -1756,11 +1790,11 @@ main(int argc, char** argv) break; case 'X': arg >> opt::missing_ratio; - opt::use_ratio=true; + opt::use_ratio = true; break; case 'Y': arg >> opt::edit_ratio; - opt::use_ratio=true; + opt::use_ratio = true; break; case 'c': arg >> opt::insertion_cap; @@ -1818,7 +1852,7 @@ main(int argc, char** argv) // check that the repeat bloom filter file is specified - RLW2019 if (opt::bloomrep_filename.empty()) { - opt::secbf = 0;//flag will track whether to query secondary Bloom filter or not + opt::secbf = 0; // flag will track whether to query secondary Bloom filter or not } else { // if the file is specified check that it is readable opt::secbf = 1; @@ -1831,10 +1865,11 @@ main(int argc, char** argv) } // added nov21 2019 XXRLW - if(opt::snv){ + if (opt::snv) { opt::max_insertions = 0; opt::max_deletions = 0; - std::cerr << PROGRAM ": EXPERIMENTAL feature note: i and d set to 0 when s is set to 1; Only tracking single-base variants.\n"; + std::cerr << PROGRAM ": EXPERIMENTAL feature note: i and d set to 0 when s is set to 1; " + "Only tracking single-base variants.\n"; } // get the basename for the file @@ -1850,7 +1885,8 @@ main(int argc, char** argv) // Load bloom filter time(&rawtime); - std::cout << "---------- loading Bloom filter from file : " << ctime(&rawtime) << "\n"; + std::cout << "---------- loading Bloom filter from file : " << ctime(&rawtime) + << "\n"; BloomFilter bloom(opt::bloom_filename.c_str()); opt::h = bloom.getHashNum(); @@ -1863,13 +1899,14 @@ main(int argc, char** argv) // assign k from Bloom filter header opt::k = bloom.getKmerSize(); - opt::insertion_cap = static_cast(static_cast(opt::k) * opt::default_insertion_cap_ratio); + opt::insertion_cap = + static_cast(static_cast(opt::k) * opt::default_insertion_cap_ratio); // print bloom filter details bloom.printBloomFilterDetails(); // Checking parameters - time(&rawtime); + time(&rawtime); std::cout << "\n---------- verifying parameters : " << ctime(&rawtime); // check that the parameters x and y are in bound if (opt::missing_threshold < 3 && opt::missing_threshold > static_cast(opt::k) && @@ -1900,10 +1937,10 @@ main(int argc, char** argv) } // print parameters: - std::cout << "\nrunning : " << PROGRAM << "\n -f " << draft_basename - << "\n -k " << opt::k << "\n -z " << opt::min_contig_len << "\n -b " - << opt::outfile_prefix << "\n -r " << bloom_basename << "\n -e " << bloomrep_basename - << "\n -i " << opt::max_insertions << "\n -d " << opt::max_deletions; + std::cout << "\nrunning : " << PROGRAM << "\n -f " << draft_basename << "\n -k " << opt::k + << "\n -z " << opt::min_contig_len << "\n -b " << opt::outfile_prefix << "\n -r " + << bloom_basename << "\n -e " << bloomrep_basename << "\n -i " << opt::max_insertions + << "\n -d " << opt::max_deletions; if (opt::use_ratio) { // RLW std::cout << "\n -X " << opt::missing_ratio << "\n -Y " << opt::edit_ratio; @@ -1911,43 +1948,43 @@ main(int argc, char** argv) std::cout << "\n -x " << opt::missing_threshold << "\n -y " << opt::edit_threshold; } - std::cout << "\n -j " << opt::jump << "\n -m " << opt::mode - << "\n -s " << opt::snv << "\n -t " << opt::nthreads << "\n -v " << opt::verbose << "\n" << std::endl; + std::cout << "\n -j " << opt::jump << "\n -m " << opt::mode << "\n -s " << opt::snv << "\n -t " + << opt::nthreads << "\n -v " << opt::verbose << "\n" + << std::endl; // Read & edit contigs time(&rawtime); if (opt::secbf) { time(&rawtime); - std::cout << "---------- loading secondary Bloom filter from file : " << ctime(&rawtime) << "\n"; - BloomFilter bloomrep(opt::bloomrep_filename.c_str()); - opt::e = bloomrep.getHashNum(); - - // Checks for the Bloom filter - if (opt::e == 0) { - std::cerr << PROGRAM ": error: secondary Bloom filter file supplied (-e) is incorrect.\n"; - exit(EXIT_FAILURE); - } + std::cout << "---------- loading secondary Bloom filter from file : " << ctime(&rawtime) + << "\n"; + BloomFilter bloomrep(opt::bloomrep_filename.c_str()); + opt::e = bloomrep.getHashNum(); + + // Checks for the Bloom filter + if (opt::e == 0) { + std::cerr << PROGRAM + ": error: secondary Bloom filter file supplied (-e) is incorrect.\n"; + exit(EXIT_FAILURE); + } // Check that primary and secondary BF kmer sizes match - if (opt::k != bloomrep.getKmerSize()) { - std::cerr << PROGRAM ": error: secondary Bloom filter k size (" - << bloomrep.getKmerSize() - << ") is different than main Bloom filter k size (" - << opt::k - << ")\n"; - exit(EXIT_FAILURE); - } + if (opt::k != bloomrep.getKmerSize()) { + std::cerr << PROGRAM ": error: secondary Bloom filter k size (" + << bloomrep.getKmerSize() << ") is different than main Bloom filter k size (" + << opt::k << ")\n"; + exit(EXIT_FAILURE); + } // print bloom filter details bloomrep.printBloomFilterDetails(); std::cout << "\n---------- reading and polishing draft : " << ctime(&rawtime); - readAndCorrect(bloom,bloomrep); + readAndCorrect(bloom, bloomrep); - } - else { + } else { std::cout << "---------- reading and polishing draft : " << ctime(&rawtime); - BloomFilter bloomrep(1000,1,1); - readAndCorrect(bloom,bloomrep); + BloomFilter bloomrep(1000, 1, 1); + readAndCorrect(bloom, bloomrep); } time(&rawtime); std::cout << "---------- process complete : " << ctime(&rawtime); From 0dc7289cef0701e1ace0f5f724321c87bf9d502d Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Fri, 3 Apr 2020 16:36:30 -0700 Subject: [PATCH 06/13] ntedit: gatk compatible vcf Former-commit-id: d4eab6e6510215c5bf4e7590cdd9d5064d5630f1 --- ntedit.cpp | 38 ++++++++++++++++++++++---------------- 1 file changed, 22 insertions(+), 16 deletions(-) diff --git a/ntedit.cpp b/ntedit.cpp index 8dc31ee..0975eb0 100644 --- a/ntedit.cpp +++ b/ntedit.cpp @@ -759,7 +759,7 @@ writeEditsToFile( vfout << contigHdr.c_str() << "\t" << pos + 1 << "\t.\t" << draft_char << "\t" << draft_char << insertion_bases.c_str() << "\t.\tPASS\tDP=" << num_support - << "\n"; + << "\tGT\t0/1\n"; insertion_bases = ""; num_support = -1; @@ -776,32 +776,38 @@ writeEditsToFile( if (substitution_record.front().altsupp1 > 0) { // XXRLWXX rfout << "\t" << substitution_record.front().altbase1 << "\t" << substitution_record.front().altsupp1; - base += ","; - base += substitution_record.front().altbase1; - support += ","; - support += std::to_string(substitution_record.front().altsupp1); + if (substitution_record.front().sub_base != substitution_record.front().altbase1) { + base += ","; + base += substitution_record.front().altbase1; + support += ","; + support += std::to_string(substitution_record.front().altsupp1); + } } if (substitution_record.front().altsupp2 > 0) { // XXRLWXX rfout << "\t" << substitution_record.front().altbase2 << "\t" << substitution_record.front().altsupp2; - base += ","; - base += substitution_record.front().altbase2; - support += ","; - support += std::to_string(substitution_record.front().altsupp2); + if (substitution_record.front().sub_base != substitution_record.front().altbase2) { + base += ","; + base += substitution_record.front().altbase2; + support += ","; + support += std::to_string(substitution_record.front().altsupp2); + } } if (substitution_record.front().altsupp3 > 0) { // XXRLWXX rfout << "\t" << substitution_record.front().altbase3 << "\t" << substitution_record.front().altsupp3; - base += ","; - base += substitution_record.front().altbase3; - support += ","; - support += std::to_string(substitution_record.front().altsupp1); + if (substitution_record.front().sub_base != substitution_record.front().altbase3) { + base += ","; + base += substitution_record.front().altbase3; + support += ","; + support += std::to_string(substitution_record.front().altsupp1); + } } rfout << "\n"; vfout << contigHdr.c_str() << "\t" << substitution_record.front().pos + 1 << "\t.\t" << substitution_record.front().draft_char << "\t" << base - << "\t.\tPASS\tDP=" << support << "\n"; + << "\t.\tPASS\tDP=" << support << "\tGT\t0/1\n"; substitution_record.pop(); } @@ -829,7 +835,7 @@ writeEditsToFile( vfout << contigHdr.c_str() << "\t" << pos << "\t.\t" << contigSeq.substr(pos - 1, (curr_node.s_pos - pos) + 1).c_str() << "\t" - << contigSeq.at(pos - 1) << "\t.\tPASS\tDP=" << curr_node.num_support << "\n"; + << contigSeq.at(pos - 1) << "\t.\tPASS\tDP=" << curr_node.num_support << "\tGT\t0/1\n"; } } } @@ -1698,7 +1704,7 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) vfout << "##source=ntEditV1.3.2" << std::endl; vfout << "##reference=file:" << opt::draft_filename << std::endl; vfout << "##INFO=" << std::endl; - vfout << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" << std::endl; + vfout << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tINTEGRATION" << std::endl; #pragma omp parallel shared(seq, dfout, rfout, vfout) { From fa18c85ec97f15f6fee1f5cfa1b0481f3c67d095 Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Fri, 3 Apr 2020 16:46:00 -0700 Subject: [PATCH 07/13] ntedit: use correct draft variable Former-commit-id: 184464ab831dd7dea910d5dc3670a85f02f410ff --- ntedit.cpp | 40 ++++++++++++++++++++++------------------ 1 file changed, 22 insertions(+), 18 deletions(-) diff --git a/ntedit.cpp b/ntedit.cpp index 0975eb0..2d56b84 100644 --- a/ntedit.cpp +++ b/ntedit.cpp @@ -776,32 +776,35 @@ writeEditsToFile( if (substitution_record.front().altsupp1 > 0) { // XXRLWXX rfout << "\t" << substitution_record.front().altbase1 << "\t" << substitution_record.front().altsupp1; - if (substitution_record.front().sub_base != substitution_record.front().altbase1) { - base += ","; - base += substitution_record.front().altbase1; - support += ","; - support += std::to_string(substitution_record.front().altsupp1); + if (substitution_record.front().draft_char != + substitution_record.front().altbase1) { + base += ","; + base += substitution_record.front().altbase1; + support += ","; + support += std::to_string(substitution_record.front().altsupp1); } } if (substitution_record.front().altsupp2 > 0) { // XXRLWXX rfout << "\t" << substitution_record.front().altbase2 << "\t" << substitution_record.front().altsupp2; - if (substitution_record.front().sub_base != substitution_record.front().altbase2) { - base += ","; - base += substitution_record.front().altbase2; - support += ","; - support += std::to_string(substitution_record.front().altsupp2); - } + if (substitution_record.front().draft_char != + substitution_record.front().altbase2) { + base += ","; + base += substitution_record.front().altbase2; + support += ","; + support += std::to_string(substitution_record.front().altsupp2); + } } if (substitution_record.front().altsupp3 > 0) { // XXRLWXX rfout << "\t" << substitution_record.front().altbase3 << "\t" << substitution_record.front().altsupp3; - if (substitution_record.front().sub_base != substitution_record.front().altbase3) { - base += ","; - base += substitution_record.front().altbase3; - support += ","; - support += std::to_string(substitution_record.front().altsupp1); - } + if (substitution_record.front().draft_char != + substitution_record.front().altbase3) { + base += ","; + base += substitution_record.front().altbase3; + support += ","; + support += std::to_string(substitution_record.front().altsupp1); + } } rfout << "\n"; @@ -835,7 +838,8 @@ writeEditsToFile( vfout << contigHdr.c_str() << "\t" << pos << "\t.\t" << contigSeq.substr(pos - 1, (curr_node.s_pos - pos) + 1).c_str() << "\t" - << contigSeq.at(pos - 1) << "\t.\tPASS\tDP=" << curr_node.num_support << "\tGT\t0/1\n"; + << contigSeq.at(pos - 1) << "\t.\tPASS\tDP=" << curr_node.num_support + << "\tGT\t0/1\n"; } } } From db1a998bf9d909589caae543479f021c142a2995 Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Tue, 7 Apr 2020 11:40:15 -0700 Subject: [PATCH 08/13] ntedit: properly assign GT Former-commit-id: 5803700d32f37b317016efc8dc13b87a1788996c --- ntedit.cpp | 87 ++++++++++++++++++++++++++++++++++++++---------------- 1 file changed, 62 insertions(+), 25 deletions(-) diff --git a/ntedit.cpp b/ntedit.cpp index 2d56b84..26e72db 100644 --- a/ntedit.cpp +++ b/ntedit.cpp @@ -759,11 +759,14 @@ writeEditsToFile( vfout << contigHdr.c_str() << "\t" << pos + 1 << "\t.\t" << draft_char << "\t" << draft_char << insertion_bases.c_str() << "\t.\tPASS\tDP=" << num_support - << "\tGT\t0/1\n"; + << "\tGT\t1/1\n"; insertion_bases = ""; num_support = -1; } + std::vector alt_base_vcf; + std::vector alt_supp_vcf; + // log all the substitutions up to this point while (!substitution_record.empty() && substitution_record.front().pos <= curr_node.e_pos) { @@ -776,41 +779,75 @@ writeEditsToFile( if (substitution_record.front().altsupp1 > 0) { // XXRLWXX rfout << "\t" << substitution_record.front().altbase1 << "\t" << substitution_record.front().altsupp1; - if (substitution_record.front().draft_char != - substitution_record.front().altbase1) { - base += ","; - base += substitution_record.front().altbase1; - support += ","; - support += std::to_string(substitution_record.front().altsupp1); - } + alt_base_vcf.emplace_back(substitution_record.front().altbase1); + alt_supp_vcf.emplace_back(substitution_record.front().altsupp1); } if (substitution_record.front().altsupp2 > 0) { // XXRLWXX rfout << "\t" << substitution_record.front().altbase2 << "\t" << substitution_record.front().altsupp2; - if (substitution_record.front().draft_char != - substitution_record.front().altbase2) { - base += ","; - base += substitution_record.front().altbase2; - support += ","; - support += std::to_string(substitution_record.front().altsupp2); - } + alt_base_vcf.emplace_back(substitution_record.front().altbase2); + alt_supp_vcf.emplace_back(substitution_record.front().altsupp2); } if (substitution_record.front().altsupp3 > 0) { // XXRLWXX rfout << "\t" << substitution_record.front().altbase3 << "\t" << substitution_record.front().altsupp3; - if (substitution_record.front().draft_char != - substitution_record.front().altbase3) { - base += ","; - base += substitution_record.front().altbase3; - support += ","; - support += std::to_string(substitution_record.front().altsupp1); - } + alt_base_vcf.emplace_back(substitution_record.front().altbase3); + alt_supp_vcf.emplace_back(substitution_record.front().altsupp3); } rfout << "\n"; + unsigned curr_best_alt_supp = 0; + char best_alt_base; + std::string best_alt_supp; + std::string genotype; + // If there are alt bases + if (alt_base_vcf.size() != 0) { + unsigned curr_best_supp = 0; + if (opt::snv) { + bool ref = false; + for (int i = 0; i < alt_base_vcf.size(); ++i) { + // Prioritize ref base over other alt base + if (substitution_record.front().draft_char == alt_base_vcf[i]) { + curr_best_alt_supp = alt_supp_vcf[i]; + ref = true; + break; + } + if (alt_supp_vcf[i] > curr_best_alt_supp) { + curr_best_alt_supp = alt_supp_vcf[i]; + best_alt_base = alt_base_vcf[i]; + } + } + best_alt_supp = std::to_string(curr_best_alt_supp); + if (ref == true) { + support = best_alt_supp + "," + support; + genotype = "0/1"; + } else { + genotype = "1/2"; + support = support + "," + best_alt_supp; + base = base + "," + best_alt_base; + } + } else { + for (int i = 0; i < alt_base_vcf.size(); ++i) { + // Skip ref base in non snv mode + if (substitution_record.front().draft_char == alt_base_vcf[i]) { + continue; + } + if (alt_supp_vcf[i] > curr_best_alt_supp) { + curr_best_alt_supp = alt_supp_vcf[i]; + best_alt_base = alt_base_vcf[i]; + } + } + best_alt_supp = std::to_string(curr_best_alt_supp); + genotype = "1/2"; + support = support + "," + best_alt_supp; + base = base + "," + best_alt_base; + } + } else { + genotype = "1/1"; + } vfout << contigHdr.c_str() << "\t" << substitution_record.front().pos + 1 << "\t.\t" << substitution_record.front().draft_char << "\t" << base - << "\t.\tPASS\tDP=" << support << "\tGT\t0/1\n"; + << "\t.\tPASS\tDP=" << support << "\tGT\t" << genotype << "\n"; substitution_record.pop(); } @@ -839,7 +876,7 @@ writeEditsToFile( vfout << contigHdr.c_str() << "\t" << pos << "\t.\t" << contigSeq.substr(pos - 1, (curr_node.s_pos - pos) + 1).c_str() << "\t" << contigSeq.at(pos - 1) << "\t.\tPASS\tDP=" << curr_node.num_support - << "\tGT\t0/1\n"; + << "\tGT\t1/1\n"; } } } @@ -1707,7 +1744,7 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep) vfout << "##fileDate=" << year << month << day << std::endl; vfout << "##source=ntEditV1.3.2" << std::endl; vfout << "##reference=file:" << opt::draft_filename << std::endl; - vfout << "##INFO=" << std::endl; + vfout << "##INFO=" << std::endl; vfout << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tINTEGRATION" << std::endl; #pragma omp parallel shared(seq, dfout, rfout, vfout) From 633883896ff98f346fefde366a0107a022b1a704 Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Tue, 7 Apr 2020 11:44:01 -0700 Subject: [PATCH 09/13] README: update output and c++ author Former-commit-id: a4f3d8b32929ceed38913e7267a1d46e17f5c8d8 --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 1c1d3ee..b318e27 100755 --- a/README.md +++ b/README.md @@ -91,7 +91,7 @@ ntedit (concept, algorithm design and prototype): Rene Warren nthits / nthash / BloomFilter.pm: Hamid Mohamadi -C++ implementation: Jessica Zhang, Rene Warren +C++ implementation: Jessica Zhang, Rene Warren, Johnathan Wong ### How to run in a pipeline @@ -324,6 +324,7 @@ Sequence reads are first shredded into kmers using ntHits, keeping track of kmer |---|---| |_changes.tsv | tab-separated file; ID bpPosition+1 OriginalBase NewBase Support k-mers (out of k/j) AlternateNewBase Alt.Support k-mers eg. U00096.3_MG1655_k12 117 A T 9| |_edited.fa | fasta file; contains the polished genome assembly | +|_variants.vcf | vcf file; contains variant calls | From 0d3f0e4136dd748f59b09e7116bccfbafb2b358a Mon Sep 17 00:00:00 2001 From: Johnathan Wong Date: Tue, 7 Apr 2020 11:46:20 -0700 Subject: [PATCH 10/13] update version information Former-commit-id: e0df0491316e8786e1cc7b1bfef9ba96604f89b9 --- README.md | 6 +++--- demo/nteditk25.time | 20 ++++++++++---------- ntedit.cpp | 4 ++-- 3 files changed, 15 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index b318e27..ba1d881 100755 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ [![Release](https://img.shields.io/github/release/bcgsc/ntEdit.svg)](https://github.com/bcgsc/ntEdit/releases) -[![Downloads](https://img.shields.io/github/downloads/bcgsc/ntEdit/total?logo=github)](https://github.com/bcgsc/ntEdit/releases/download/v1.3.1/ntEdit_v1-3-1.tar.gz) +[![Downloads](https://img.shields.io/github/downloads/bcgsc/ntEdit/total?logo=github)](https://github.com/bcgsc/ntEdit/releases/download/v1.3.2/ntEdit_v1-3-2.tar.gz) [![Conda](https://img.shields.io/conda/dn/bioconda/ntedit?label=Conda)](https://anaconda.org/bioconda/ntedit) [![Issues](https://img.shields.io/github/issues/bcgsc/ntEdit.svg)](https://github.com/bcgsc/ntEdit/issues) @@ -21,7 +21,7 @@ ntEdit is a fast and scalable genomics application for polishing genome assembly It simplifies polishing and "haploidization" of gene and genome sequences with its re-usable Bloom filter design. We expect ntEdit to have additional applications in fast mapping of simple nucleotide variations between any two individuals or species’ genomes. ```diff -! NOTE: In v1.3.1 the parameter k is automatically detected from supplied Bloom filters +! NOTE: In v1.3.1 onwards, the parameter k is automatically detected from supplied Bloom filters ``` ### Implementation and requirements @@ -161,7 +161,7 @@ eg.
 e.g. ./ntedit -f ecoliWithMismatches001Indels0001.fa -r solidBF_k25.bf -b ntEditEcolik25
 
-ntEdit v1.3.1
+ntEdit v1.3.2
 
 Scalable genome sequence polishing.
 
diff --git a/demo/nteditk25.time b/demo/nteditk25.time
index 7588e82..8e5f5a6 100644
--- a/demo/nteditk25.time
+++ b/demo/nteditk25.time
@@ -1,21 +1,21 @@
-	Command being timed: "../ntedit -f ecoliWithMismatches001Indels0001.fa.gz -r solidBF_k25.bf -d 5 -i 4 -b nteditk25"
-	User time (seconds): 0.49
-	System time (seconds): 0.04
-	Percent of CPU this job got: 95%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.56
+	Command being timed: "../ntedit -f /projects/btl/jowong/github/ntEdit/demo/ecoliWithMismatches001Indels0001.fa.gz -r solidBF_k25.bf -d 5 -i 4 -b nteditk25"
+	User time (seconds): 0.58
+	System time (seconds): 0.03
+	Percent of CPU this job got: 93%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.66
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 31624
+	Maximum resident set size (kbytes): 31632
 	Average resident set size (kbytes): 0
 	Major (requiring I/O) page faults: 0
-	Minor (reclaiming a frame) page faults: 7961
-	Voluntary context switches: 449
-	Involuntary context switches: 143
+	Minor (reclaiming a frame) page faults: 7963
+	Voluntary context switches: 109
+	Involuntary context switches: 79
 	Swaps: 0
 	File system inputs: 0
-	File system outputs: 9408
+	File system outputs: 9928
 	Socket messages sent: 0
 	Socket messages received: 0
 	Signals delivered: 0
diff --git a/ntedit.cpp b/ntedit.cpp
index 26e72db..e467bc4 100644
--- a/ntedit.cpp
+++ b/ntedit.cpp
@@ -30,13 +30,13 @@ KSEQ_INIT(gzFile, gzread)
 
 // NOLINTNEXTLINE(modernize-avoid-c-arrays)
 static const char VERSION_MESSAGE[] =
-    PROGRAM " version 1.3.1\n"
+    PROGRAM " version 1.3.2\n"
             "written by Rene Warren, Hamid Mohamadi, and Jessica Zhang.\n"
             "copyright 2018-2020 Canada's Michael smith Genome Science Centre\n";
 
 // NOLINTNEXTLINE(modernize-avoid-c-arrays)
 static const char USAGE_MESSAGE[] = PROGRAM
-    " v1.3.1\n"
+    " v1.3.2\n"
     "\n"
     "Scalable genome sequence polishing.\n"
     "\n"

From 247bfd60a0502780845630f9001fc3f7e9f5bbd9 Mon Sep 17 00:00:00 2001
From: Johnathan Wong 
Date: Tue, 7 Apr 2020 11:46:45 -0700
Subject: [PATCH 11/13] demo: add vcf output

Former-commit-id: ba2f2b12738ef41f5211ac228055fef31514f8e2
---
 demo/nteditk25_variants.vcf | 4998 +++++++++++++++++++++++++++++++++++
 1 file changed, 4998 insertions(+)
 create mode 100644 demo/nteditk25_variants.vcf

diff --git a/demo/nteditk25_variants.vcf b/demo/nteditk25_variants.vcf
new file mode 100644
index 0000000..489d8d5
--- /dev/null
+++ b/demo/nteditk25_variants.vcf
@@ -0,0 +1,4998 @@
+##fileformat=VCFv4.2
+##fileDate=20200407
+##source=ntEditV1.3.2
+##reference=file:/projects/btl/jowong/github/ntEdit/demo/ecoliWithMismatches001Indels0001.fa.gz
+##INFO=
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	INTEGRATION
+U00096.3_MG1655_k12	117	.	A	T	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	2308	.	G	A	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	3084	.	T	G	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	3970	.	A	G	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	5016	.	C	A	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	5159	.	A	G	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	5214	.	G	A	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	6444	.	G	A	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	8740	.	G	C	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	11394	.	C	G	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	11525	.	G	C	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	12660	.	T	A	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	14429	.	C	G	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	15471	.	G	A	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	15659	.	C	T	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	16199	.	A	C	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	16646	.	C	T	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	16971	.	C	T	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	17203	.	G	T	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	18961	.	G	A	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	19556	.	G	A	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	20310	.	C	G	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	20731	.	C	T	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	21954	.	A	G	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	22272	.	C	T	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	23190	.	C	A	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	23832	.	G	A	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	26514	.	A	G	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	26559	.	G	A	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	27678	.	C	T	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	28443	.	T	G	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	29520	.	CAT	C	.	PASS	DP=8	GT	1/1
+U00096.3_MG1655_k12	29834	.	C	G	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	30612	.	G	A	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	31002	.	A	G	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	31337	.	G	C	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	31756	.	G	A	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	32638	.	G	C	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	32767	.	A	T	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	33313	.	C	T	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	34206	.	G	C	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	34526	.	C	A	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	35056	.	A	G	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	41665	.	T	C	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	42082	.	C	T	.	PASS	DP=9	GT	1/1
+U00096.3_MG1655_k12	43042	.	C	T	.	PASS	DP=9	GT	1/1
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+U00096.3_MG1655_k12	2346227	.	T	C	.	PASS	DP=9	GT	1/1
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+U00096.3_MG1655_k12	2376124	.	AATCGA	A	.	PASS	DP=8	GT	1/1
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+U00096.3_MG1655_k12	2485671	.	G	GAA	.	PASS	DP=8	GT	1/1
+U00096.3_MG1655_k12	2486600	.	GAG	G	.	PASS	DP=8	GT	1/1
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From 8c28d83ac79955d984b401fb3b55f91ea0df9e76 Mon Sep 17 00:00:00 2001
From: Johnathan Wong 
Date: Tue, 7 Apr 2020 12:10:24 -0700
Subject: [PATCH 12/13] ntedit: fix clang-tidy errors

Former-commit-id: 3088a9d18e4935081cb66da7abbce9c2b72cc7b0
---
 ntedit.cpp | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/ntedit.cpp b/ntedit.cpp
index e467bc4..ff7f8d9 100644
--- a/ntedit.cpp
+++ b/ntedit.cpp
@@ -800,7 +800,7 @@ writeEditsToFile(
 				std::string best_alt_supp;
 				std::string genotype;
 				// If there are alt bases
-				if (alt_base_vcf.size() != 0) {
+				if (!alt_base_vcf.empty()) {
 					unsigned curr_best_supp = 0;
 					if (opt::snv) {
 						bool ref = false;
@@ -817,13 +817,16 @@ writeEditsToFile(
 							}
 						}
 						best_alt_supp = std::to_string(curr_best_alt_supp);
-						if (ref == true) {
-							support = best_alt_supp + "," + support;
+						if (ref) {
+							support.append(",");
+							support.append(best_alt_supp);
 							genotype = "0/1";
 						} else {
 							genotype = "1/2";
-							support = support + "," + best_alt_supp;
-							base = base + "," + best_alt_base;
+							support += ",";
+							support += best_alt_supp;
+							base += ",";
+							base += best_alt_base;
 						}
 					} else {
 						for (int i = 0; i < alt_base_vcf.size(); ++i) {
@@ -838,8 +841,10 @@ writeEditsToFile(
 						}
 						best_alt_supp = std::to_string(curr_best_alt_supp);
 						genotype = "1/2";
-						support = support + "," + best_alt_supp;
-						base = base + "," + best_alt_base;
+						support += ",";
+						support += best_alt_supp;
+						base += ",";
+						base += best_alt_base;
 					}
 				} else {
 					genotype = "1/1";

From 3e48c0d1b561950805ef34601700a992c6ce9049 Mon Sep 17 00:00:00 2001
From: Johnathan Wong 
Date: Tue, 7 Apr 2020 12:13:49 -0700
Subject: [PATCH 13/13] ntedit: fix clang-tidy errors

Former-commit-id: ba6bee1a9a4ca5d083fc3b14205949e227adc738
---
 ntedit.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ntedit.cpp b/ntedit.cpp
index ff7f8d9..1fef9d6 100644
--- a/ntedit.cpp
+++ b/ntedit.cpp
@@ -796,7 +796,7 @@ writeEditsToFile(
 				}
 				rfout << "\n";
 				unsigned curr_best_alt_supp = 0;
-				char best_alt_base;
+				char best_alt_base = '1';
 				std::string best_alt_supp;
 				std::string genotype;
 				// If there are alt bases