Handle when seq is both ref and query

mooreryan · May 16, 2017 · 4cb98fe · 4cb98fe
1 parent 2bf0a3a
commit 4cb98fe
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Showing 4 changed files with 45 additions and 13 deletions.
diff --git a/src/pasv.c b/src/pasv.c
@@ -109,21 +109,29 @@ get_aln_posns(char* aln_outfile,
                  seq_header);
 
     if (tmp_rseq->first_ref_seq == 1) {
-      assert(tmp_rseq->query_seq != 1);
-      assert(first_ref_seq_found == 0);
-      first_ref_seq_found = 1;
+      ++first_ref_seq_found;
+      PANIC_IF(first_ref_seq_found > 1,
+               STD_ERR,
+               stderr,
+               "Found more than one key ref seq (%s) in file '%s'\n",
+               seq->name.s,
+               aln_outfile);
 
       first_ref_seq = rseq_init(seq);
-    } else if (tmp_rseq->query_seq == 1) {
-      assert(query_seq_found == 0);
-
-      query_seq_found = 1;
-      query_seq = rseq_init(seq);
     }
 
-    if (first_ref_seq_found == 1 && query_seq_found == 1) {
-      free(seq_header);
-      break;
+    if (tmp_rseq->query_seq == 1) {
+      ++query_seq_found;
+
+      PANIC_IF((query_seq_found > 1 && first_ref_seq_found == 0) ||
+               (query_seq_found > 2 && first_ref_seq_found == 1),
+               STD_ERR,
+               stderr,
+               "Found more than one query seq (%s) in file '%s'\n",
+               seq->name.s,
+               aln_outfile);
+
+      query_seq = rseq_init(seq);
     }
 
     free(seq_header);
@@ -224,7 +232,7 @@ main(int argc, char *argv[])
   char* query_fname = NULL;
 
   static char version_banner[] =
-    "  Version: 0.0.3\n"
+    "  Version: 0.0.4\n"
     "  Copyright: 2017 Ryan Moore\n"
     "  Contact: [email protected]\n"
     "  Website: https://github.com/mooreryan/pasv\n"
@@ -598,7 +606,7 @@ main(int argc, char *argv[])
 
   fprintf(outfs, "name\ttype\tspans\toligo");
   for (int n = 0; n < num_key_posns; ++n) {
-    fprintf(outfs, "\tpos.%d", key_posns[n]);
+    fprintf(outfs, "\tpos.%d", key_posns[n] + 1);
   }
   fprintf(outfs, "\n");
   int num_ref_seqs = tommy_array_size(ref_seqs);

diff --git a/src/rseq.c b/src/rseq.c
@@ -171,6 +171,20 @@ rseq_try_insert_hashlin(rseq_t* rseq, tommy_hashlin* hash)
              "Header '%s' is repeated, but the sequences it "
              "represents are not equal.",
              rseq->head);
+
+    /* Sometimes a seq can be repeated in both the ref and query
+       files. In this case it's possible that it could be the first
+       ref seq AND a query seq. */
+    /* Now, check if the first_ref_seq and query_seq flags match. If
+       not, the rseq flag will be added to the tmp seq's flag */
+    if (rseq->first_ref_seq == 1 && tmp->first_ref_seq == 0) {
+      tmp->first_ref_seq = 1; /* set it to match the incoming rseq */
+    }
+
+    if (rseq->query_seq == 1 && tmp->query_seq == 0) {
+      tmp->query_seq = 1;
+    }
+
   } else {
     tommy_hashlin_insert(hash,
                          &rseq->node,

diff --git a/test_files/queries.fa b/test_files/queries.fa
@@ -2,3 +2,9 @@
 MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGKRFGSHALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQREGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH
 >2 query
 MSNNRPLLLLIDGHALAYRAFHALAEAGLRSSTGEPTYAVFGFTSAMLNAIEEYHPDYAAVAFDVGKTFRDDLYAEYKANRAETPAEFEQQLERIKQVLAAFDIPIYTADGYEADDVIGTLARQATERGVDVLILTGDTDTLQLVDEHVTVLLNNPYVRGSKNTTRYGVADVCARYKGLRPDQLADLRGLKGDPSDNIPGVKGIGEAGAIALLNQFGSIENLYDHLDEAPKRYQKHLEGQRDAALFSKKLATIVRDAPVTLDLPAATLADYDRSRVIAVFQELEFGASLVRRLPPSQTIAAPQALPPVEPPAPLQVDMFAPATPGPDDGPQQLTLFNDMPTPVAPVVEPPAHDAPGEYRAACNDADLEAIVTELKHASLFAFDTETRGTNPLRDDLVGIALATIPGSGWYVPLGHTTGEAQLPRERVIAALRPFFADPARSRIAHNAKFDIEVLERAGIPVAGVAFDTMLAAALLDKRRNLKDLAFYELNLAAPLESIEALIGKGKNQVTFADVPIARATPYAAADADMTLRLKPALEAKLRAAGSVADVFYRLEMPLVPVLVRMEQAGILLDVPYMRALGERMGRELEQIEQQIYAIAGQTFNINSGDQLSEVLFGPKINLPTTGLDRTRTGRYSLTAQALEELQASDTTGIIELILRHRRLSKLKSTYVDELPALVNPETGRVHTDYNQLGAATGRLSSNSPNLQNIPTRTEEGREVRRGFIAAPGHLLIAADYSQIELRVLAHMTGDPNLIQTFIEGRDIHAATAARLFGVGFSAVDKNQRRIAKTVVFGVIYGISPFGLAQRLGISREQARGLIDSLFDQFPRIRDYIDRTLDIGRSEGYVQSLFGRRRPMFDLRVSGPRRQAAEREAINHPIQSTAADIMKLAMIAVDAELQRRQMRTRMLLQVHDELIFEAPEAEVDDVVALVRERMEGVLHGMEPPFAVPLRVEIETGPNWEELTPAG
+>1_e_coli ref
+MVQIPQNPLILVDGSSYLYRAYHAFPPLTNSAGEPTGAMYGVLNMLRSLIMQYKPTHAAVVFDAKGKTFRDELFEHYKSHRPPMPDDLRAQIEPLHAMVKAMGLPLLAVSGVEADDVIGTLAREAEKAGRPVLISTGDKDMAQLVTPNITLINTMTNTILGPEEVVNKYGVPPELIIDFLALMGDSSDNIPGVPGVGEKTAQALLQGLGGLDTLYAEPEKIAGLSFRGAKTMAAKLEQNKEVAYLSYQLATIKTDVELELTCEQLEVQPPAAEELLGLFKKYEFKRWTADVEAGKWLQAKGVKPAARPQETSVADEAPEVTATVISYDNYVTILDEETLKEWIAKLEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPKVILEYRGLAKLKSTYTDKLPLMINPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYVIVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAFGLARQLNIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGRRLYLPDIKSSNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQVHDELVFEVHKDDVDAVAKQIHQLMENCTRLDVPLLVEVGSGENWDQAH
+>2_phage ref
+MLYPWENMYASDIETTGLLEQMRKQAAPRLHNIGYIDVLTREETVIEWTDRKSIQAFLDTGPTLIMHNGATFDFEALRFLGYDVSKCTLIDTLFISWYLQPRRVKHGLEGYGEEFGVPKPVIEDWENQTQEEYNHRVMEDCKIQLKLWEQQYIQLLKIYKSPSEVKRFVEYLMTKARQQVIQQRTRWKLNIEKALAFKAKLEPMIKEKTDALEASMPRIPEYVIKTRPAKCHKMNGQLSATGIKWKAVCDANGLDWKDPDLAIKVLKGYKEPNAGSHVQIKDWLFSLGWEPETFKFDRNKETGETRQIPQITVKDEDGNPEICPSLHKLAERNPESGIQHLIGMGVYKHRLSVVNGFLRDVDEDGYLTARCGGLTNTLRLKHRELVNLPSIRVFGGEELRSMLEAWREDYEQLGSDLCSLEDRCKHHFQWMYDPEYVKKQLAPDYDAHLAIGVIGGFITEQESQDHKDGIKKCKQRPMFKTTNYACQYGAGVPTVARSAGCDQTTAARLHKAYWDLNWSIKEIAANTKVITVDGQMWQQNPVNKFWYSLRTEKDRFSTLCQGTGAYVFDIWCNNIIAICNERWGCDPLLSGQFHDELILQVKKGFRDLWTDLLNEAMDRTNKELKLNRDCACDVQFGDNYAEIH
+>1 query
+MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGKRFGSHALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQREGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH
diff --git a/test_files/refs.fa b/test_files/refs.fa
@@ -2,3 +2,7 @@
 MVQIPQNPLILVDGSSYLYRAYHAFPPLTNSAGEPTGAMYGVLNMLRSLIMQYKPTHAAVVFDAKGKTFRDELFEHYKSHRPPMPDDLRAQIEPLHAMVKAMGLPLLAVSGVEADDVIGTLAREAEKAGRPVLISTGDKDMAQLVTPNITLINTMTNTILGPEEVVNKYGVPPELIIDFLALMGDSSDNIPGVPGVGEKTAQALLQGLGGLDTLYAEPEKIAGLSFRGAKTMAAKLEQNKEVAYLSYQLATIKTDVELELTCEQLEVQPPAAEELLGLFKKYEFKRWTADVEAGKWLQAKGVKPAARPQETSVADEAPEVTATVISYDNYVTILDEETLKEWIAKLEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPKVILEYRGLAKLKSTYTDKLPLMINPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYVIVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAFGLARQLNIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGRRLYLPDIKSSNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQVHDELVFEVHKDDVDAVAKQIHQLMENCTRLDVPLLVEVGSGENWDQAH
 >2_phage ref
 MLYPWENMYASDIETTGLLEQMRKQAAPRLHNIGYIDVLTREETVIEWTDRKSIQAFLDTGPTLIMHNGATFDFEALRFLGYDVSKCTLIDTLFISWYLQPRRVKHGLEGYGEEFGVPKPVIEDWENQTQEEYNHRVMEDCKIQLKLWEQQYIQLLKIYKSPSEVKRFVEYLMTKARQQVIQQRTRWKLNIEKALAFKAKLEPMIKEKTDALEASMPRIPEYVIKTRPAKCHKMNGQLSATGIKWKAVCDANGLDWKDPDLAIKVLKGYKEPNAGSHVQIKDWLFSLGWEPETFKFDRNKETGETRQIPQITVKDEDGNPEICPSLHKLAERNPESGIQHLIGMGVYKHRLSVVNGFLRDVDEDGYLTARCGGLTNTLRLKHRELVNLPSIRVFGGEELRSMLEAWREDYEQLGSDLCSLEDRCKHHFQWMYDPEYVKKQLAPDYDAHLAIGVIGGFITEQESQDHKDGIKKCKQRPMFKTTNYACQYGAGVPTVARSAGCDQTTAARLHKAYWDLNWSIKEIAANTKVITVDGQMWQQNPVNKFWYSLRTEKDRFSTLCQGTGAYVFDIWCNNIIAICNERWGCDPLLSGQFHDELILQVKKGFRDLWTDLLNEAMDRTNKELKLNRDCACDVQFGDNYAEIH
+>1_e_coli ref
+MVQIPQNPLILVDGSSYLYRAYHAFPPLTNSAGEPTGAMYGVLNMLRSLIMQYKPTHAAVVFDAKGKTFRDELFEHYKSHRPPMPDDLRAQIEPLHAMVKAMGLPLLAVSGVEADDVIGTLAREAEKAGRPVLISTGDKDMAQLVTPNITLINTMTNTILGPEEVVNKYGVPPELIIDFLALMGDSSDNIPGVPGVGEKTAQALLQGLGGLDTLYAEPEKIAGLSFRGAKTMAAKLEQNKEVAYLSYQLATIKTDVELELTCEQLEVQPPAAEELLGLFKKYEFKRWTADVEAGKWLQAKGVKPAARPQETSVADEAPEVTATVISYDNYVTILDEETLKEWIAKLEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPKVILEYRGLAKLKSTYTDKLPLMINPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYVIVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAFGLARQLNIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGRRLYLPDIKSSNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQVHDELVFEVHKDDVDAVAKQIHQLMENCTRLDVPLLVEVGSGENWDQAH
+>2_phage ref
+MLYPWENMYASDIETTGLLEQMRKQAAPRLHNIGYIDVLTREETVIEWTDRKSIQAFLDTGPTLIMHNGATFDFEALRFLGYDVSKCTLIDTLFISWYLQPRRVKHGLEGYGEEFGVPKPVIEDWENQTQEEYNHRVMEDCKIQLKLWEQQYIQLLKIYKSPSEVKRFVEYLMTKARQQVIQQRTRWKLNIEKALAFKAKLEPMIKEKTDALEASMPRIPEYVIKTRPAKCHKMNGQLSATGIKWKAVCDANGLDWKDPDLAIKVLKGYKEPNAGSHVQIKDWLFSLGWEPETFKFDRNKETGETRQIPQITVKDEDGNPEICPSLHKLAERNPESGIQHLIGMGVYKHRLSVVNGFLRDVDEDGYLTARCGGLTNTLRLKHRELVNLPSIRVFGGEELRSMLEAWREDYEQLGSDLCSLEDRCKHHFQWMYDPEYVKKQLAPDYDAHLAIGVIGGFITEQESQDHKDGIKKCKQRPMFKTTNYACQYGAGVPTVARSAGCDQTTAARLHKAYWDLNWSIKEIAANTKVITVDGQMWQQNPVNKFWYSLRTEKDRFSTLCQGTGAYVFDIWCNNIIAICNERWGCDPLLSGQFHDELILQVKKGFRDLWTDLLNEAMDRTNKELKLNRDCACDVQFGDNYAEIH