Updated version number

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.63])
-AC_INIT([ivar], [1.2.5], [[email protected]])
+AC_INIT([ivar], [1.3], [[email protected]])
 AM_INIT_AUTOMAKE([foreign subdir-objects])
 AC_CONFIG_HEADERS([config.h])
 

src/ivar.cpp

@@ -16,7 +16,7 @@
 #include "suffix_tree.h"
 #include "get_common_variants.h"
 
-const std::string VERSION = "1.2.5";
+const std::string VERSION = "1.3";
 
 struct args_t {
   std::string bam;		// -i
@@ -201,7 +201,7 @@ int main(int argc, char* argv[]){
     if(i != argc-1)
       cl_cmd << " ";
   }
-  cl_cmd << "\n\0";  
+  cl_cmd << "\n\0";
   std::string cmd(argv[1]);
   if(cmd.compare("-v") == 0){
     print_version_info();
@@ -212,7 +212,7 @@ int main(int argc, char* argv[]){
   argv[1] = argv[0];
   argv++;
   argc--;
-  // ivar trim 
+  // ivar trim
   if (cmd.compare("trim") == 0){
     g_args.min_qual = 20;
     g_args.sliding_window = 4;
@@ -265,7 +265,7 @@ int main(int argc, char* argv[]){
     }
     g_args.prefix = get_filename_without_extension(g_args.prefix,".bam");
     res = trim_bam_qual_primer(g_args.bam, g_args.bed, g_args.prefix, g_args.region, g_args.min_qual, g_args.sliding_window, cl_cmd.str(), g_args.write_no_primers_flag, g_args.keep_for_reanalysis, g_args.min_length, g_args.primer_pair_file);
-  } 
+  }
   // ivar variants
   else if (cmd.compare("variants") == 0){
     g_args.min_qual = 20;
@@ -323,7 +323,7 @@ int main(int argc, char* argv[]){
       return -1;
     }
     res = call_variants_from_plup(std::cin, g_args.prefix, g_args.min_qual, g_args.min_threshold, g_args.min_depth, g_args.ref, g_args.gff);
-  } 
+  }
   // ivar consensus
   else if (cmd.compare("consensus") == 0){
     opt = getopt( argc, argv, consensus_opt_str);
@@ -494,7 +494,7 @@ int main(int argc, char* argv[]){
 	break;
       case 'f':
 	g_args.primer_pair_file = optarg;
-	break;	
+	break;
       case 'p':
 	g_args.prefix = optarg;
 	break;

tests/test_amplicon_search.cpp

@@ -7,41 +7,41 @@
 
 int test_amplicon_search(std::string bam_file, std::string bed_file, std::string pair_info_file, bool expected[])
 {
-    std::vector<primer> primers;
-    IntervalTree amplicons;
-    primers = populate_from_file(bed_file);
-    std::cout << "Total Number of primers: " << primers.size() << std::endl;
-    amplicons = populate_amplicons(pair_info_file, primers);
-    samFile *in = hts_open(bam_file.c_str(), "r");
-    sam_hdr_t *hdr = sam_hdr_read(in);
-    bam1_t *aln = bam_init1();
-    int cnt = 0;
-    int res = 0;
-    while(sam_read1(in, hdr, aln) >= 0) {
-        res = amplicon_filter(amplicons, aln);
-        if(res != expected[cnt]){
-           	std::cout << "Amplicon filter output did not match " << bam_get_qname(aln)  << " Expected " <<  expected[cnt]  << " " 
-               << "Got " << res << std::endl;
-            std::cout << "Read intervals: " << aln->core.pos << ":" << bam_endpos(aln) << std::endl;
-            return -1;
-        }
-        cnt++;
+  std::vector<primer> primers;
+  IntervalTree amplicons;
+  primers = populate_from_file(bed_file);
+  std::cout << "Total Number of primers: " << primers.size() << std::endl;
+  amplicons = populate_amplicons(pair_info_file, primers);
+  samFile *in = hts_open(bam_file.c_str(), "r");
+  sam_hdr_t *hdr = sam_hdr_read(in);
+  bam1_t *aln = bam_init1();
+  int cnt = 0;
+  int res = 0;
+  while(sam_read1(in, hdr, aln) >= 0) {
+    res = amplicon_filter(amplicons, aln);
+    if(res != expected[cnt]){
+      std::cout << "Amplicon filter output did not match " << bam_get_qname(aln)  << " Expected " <<  expected[cnt]  << " "
+		<< "Got " << res << std::endl;
+      std::cout << "Read intervals: " << aln->core.pos << ":" << bam_endpos(aln) << std::endl;
+      return -1;
     }
-    return 0;
+    cnt++;
+  }
+  return 0;
 }
 
 
 int main(){
-    int success;
-    std::string bam = "../data/test_amplicon.sorted.bam";
-    std::string pair_indice = "../data/pair_info_2.tsv";
-    std::string bed = "../data/test_isize.bed";
-    std::string prefix = "/tmp/data/trim_amplicon";
-    std::string bam_out = "/tmp/trim_amplicon.bam";
+  int success;
+  std::string bam = "../data/test_amplicon.sorted.bam";
+  std::string pair_indice = "../data/pair_info_2.tsv";
+  std::string bed = "../data/test_isize.bed";
+  std::string prefix = "/tmp/data/trim_amplicon";
+  std::string bam_out = "/tmp/trim_amplicon.bam";
 
-    IntervalTree amplicons;
-    bool expected[8] = {true, false, true, false, true, false, true, false};
-    success = test_amplicon_search(bam, bed, pair_indice, expected);
-    amplicons.inOrder();    
-    return success;
-}
+  IntervalTree amplicons;
+  bool expected[8] = {true, false, true, false, true, false, true, false};
+  success = test_amplicon_search(bam, bed, pair_indice, expected);
+  amplicons.inOrder();
+  return success;
+}