HPG-Methyl version 3.1.

Changelog:

- Now the methylation context generated when using the --write-mcontext
  option is stored in both per-context CSV files and in the optional
  tag fields of the BAM file alignments, following the Bismark naming
  convention. Check the user manual for more information on the new SAM
  tags.

- Several bugfixes involving memory leaks and unused memory-

- Minor performance optimizations.

SConstruct

@@ -35,7 +35,7 @@ SConscript(['%s/SConscript' % bioinfo_path,
             '%s/SConscript' % commons_path
             ], exports = ['env', 'debug', 'compiler'])
 
-env.Program('#bin/hpg-aligner',
+env.Program('#bin/hpg-methyl',
              source = [Glob('src/*.c'),
 	               Glob('src/build-index/*.c'),
 	               Glob('src/dna/*.c'),

lib/bioinfo-libs/aligners/bwt/bwt.c

@@ -891,7 +891,7 @@ size_t bwt_map_exact_seq(char *seq,
   //replaceBases(seq, code_seq, len);
   bwt_encode_Bases(code_seq, seq, len, &index->table);
   struct timeval t_start, t_end;
-  char *optional_fields /*= (char *)malloc(sizeof(char)*256)*/;
+  char *optional_fields = NULL;
   //printf("---> EXACT Search Read (%d): %s\n", len, seq);
 
 
@@ -1897,39 +1897,27 @@ size_t __bwt_map_inexact_read(fastq_read_t *read,
 //-----------------------------------------------------------------------------
 
 alignment_t* add_optional_fields(alignment_t *alignment, size_t n_mappings) {
-  char *p, *optional_fields;
-  size_t optional_fields_length = 100;
-  int distance;
-  int AS = 254;
-  int cigar_len;
-
-  optional_fields = (char *)calloc(optional_fields_length, sizeof(char));
-  p = optional_fields;
-
-  sprintf(p, "ASi");
-  p += 3;
-  memcpy(p, &AS, sizeof(int));
-  p += sizeof(int);
-
-  sprintf(p, "NHi");
-  p += 3;
-  memcpy(p, &n_mappings, sizeof(int));
-  p += sizeof(int);
-
-  sprintf(p, "NMi");
-  p += 3;
-  cigar_len = strlen(alignment->cigar);
-
-  if (alignment->cigar[cigar_len - 1] == '=') {
+  bam_int_t distance;
+  bam_int_t AS = 254;
+  bam_int_t NH = n_mappings;
+
+  bam_tag_t* as_tag = bam_tag_init(AS_TAG_NAME, BAM_TAG_TYPE_INT, 0, 0);
+  bam_tag_t* nh_tag = bam_tag_init(NH_TAG_NAME, BAM_TAG_TYPE_INT, 0, 0);
+  bam_tag_t* nm_tag = bam_tag_init(NM_TAG_NAME, BAM_TAG_TYPE_INT, 0, 0);
+
+  if (alignment->cigar[strlen(alignment->cigar) - 1] == '=') {
     distance = 0;
   } else {
     distance = 1;
   }
-
-  memcpy(p, &distance, sizeof(int));
-  p += sizeof(int);
-  alignment->optional_fields_length = p - optional_fields;
-  alignment->optional_fields = optional_fields;
+
+  bam_tag_set_scalar(as_tag, &AS);
+  bam_tag_set_scalar(nh_tag, &NH);
+  bam_tag_set_scalar(nm_tag, &distance);
+
+  array_list_insert(as_tag, alignment->optional_tags);
+  array_list_insert(nh_tag, alignment->optional_tags);
+  array_list_insert(nm_tag, alignment->optional_tags);
 
   return alignment;
 }