- Removed legacy unsupported options from the help to avoid users

  from crashing the application.
- Fixed a bug in the Smith-Waterman aligner which clamped the
  reported alignment score in the tags to 0 or 254. The MAPQ
  score was correct.

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

@@ -199,8 +199,9 @@ interval_t* __bwt_map_inexact_read_bs_new(fastq_read_t *read,
   size_t len = end_read - start_read + 1;
   size_t len_calc = len;
 
-  //Only a entire read can be mapped, if not the read will be included in an anchor
+  // Only a entire read can be mapped, if not the read will be included in an anchor
   bool mapp = true;
+
   if (len < total_read_len) {
     mapp = false;
   }

src/options.c

@@ -330,18 +330,18 @@ void** argtable_options_new(void) {
      argtable[2] = arg_int0("l", "log-level", NULL, "Log debug level");
      argtable[3] = arg_lit0(NULL, "report-all", "Report all alignments");
      argtable[4] = arg_file0("o", "outdir", NULL, "Output directory");
-     argtable[5] = arg_int0(NULL, "gpu-threads", NULL, "(OBSOLETE) Number of GPU Threads");
+     argtable[5] = arg_int0(NULL, " ", NULL, " ");
      argtable[6] = arg_int0(NULL, "cpu-threads", NULL, "Number of CPU Threads");
      argtable[7] = arg_int0("r", "index-ratio", NULL, "BWT index compression ratio");
-     argtable[8] = arg_int0(NULL, "cal-seeker-errors", NULL, "(OBSOLETE) Number of errors in CAL Seeker");
+     argtable[8] = arg_int0(NULL, " ", NULL, " ");
      argtable[9] = arg_int0(NULL, "min-cal-size", NULL, "Minimum CAL size");
      argtable[10] = arg_int0(NULL, "max-distance-seeds", NULL, "Maximum distance between seeds");
      argtable[11] = arg_int0(NULL, "read-batch-size", NULL, "Batch Size");
      argtable[12] = arg_int0(NULL, "write-batch-size", NULL, "Write Size");
-     argtable[13] = arg_int0(NULL, "num-cal-seekers", NULL, "(OBSOLETE) Number of CAL Seekers");
-     argtable[14] = arg_int0(NULL, "extra-seed-left-padding", NULL, "(OBSOLETE) Nucleotides padding of left min seed");
-     argtable[15] = arg_int0(NULL, "extra-seed-right-padding", NULL, "(OBSOLETE) Nucleotides padding of right min seed");
-     argtable[16] = arg_file0(NULL, "transcriptome-file", NULL, "(OBSOLETE) Transcriptome file to help search splice junctions");
+     argtable[13] = arg_int0(NULL, " ", NULL, " ");
+     argtable[14] = arg_int0(NULL, " ", NULL, " ");
+     argtable[15] = arg_int0(NULL, " ", NULL, " ");
+     argtable[16] = arg_file0(NULL, " ", NULL, " ");
      argtable[17] = arg_int0(NULL, "seed-size", NULL, "Number of nucleotides in a seed");
      argtable[18] = arg_int0(NULL, "min-seed-size", NULL, "Minimum number of nucleotides in a seed");
      argtable[19] = arg_int0(NULL, "cal-flank-size", NULL, "Flank length for CALs");
@@ -350,23 +350,23 @@ void** argtable_options_new(void) {
      argtable[22] = arg_dbl0(NULL, "sw-gap-open", NULL, "Gap open penalty for Smith-Waterman algorithm");
      argtable[23] = arg_dbl0(NULL, "sw-gap-extend", NULL, "Gap extend penalty for Smith-Waterman algorithm");
      argtable[24] = arg_dbl0(NULL, "sw-min-score", NULL, "Minimum score for valid mappings");
-     argtable[25] = arg_int0(NULL, "max-intron-size", NULL, "(OBSOLETE) Maximum intron size");
-     argtable[26] = arg_int0(NULL, "min-intron-size", NULL, "(OBSOLETE) Minimum intron size");
+     argtable[25] = arg_int0(NULL, " ", NULL, " ");
+     argtable[26] = arg_int0(NULL, " ", NULL, " ");
      argtable[27] = arg_lit0("t", "time", "Timming mode active");
      argtable[28] = arg_lit0("s", "stats", "Statistics mode active");
      argtable[29] = arg_lit0("h", "help", "Help option");
      argtable[30] = arg_str0(NULL, "prefix", NULL, "File prefix name");
      argtable[31] = arg_file0("g", "ref-genome", NULL, "Reference genome");
-     argtable[32] = arg_file0("j", "fq2,fastq2", NULL, "(OBSOLETE) Reads file input #2 (for paired mode)");
-     argtable[33] = arg_int0(NULL, "paired-mode", NULL, "(OBSOLETE) Pair mode: 0 = single-end, 1 = paired-end, 2 = mate-pair [Default 0]");
-     argtable[34] = arg_int0(NULL, "paired-min-distance", NULL, "(OBSOLETE) Minimum distance between pairs");
-     argtable[35] = arg_int0(NULL, "paired-max-distance", NULL, "(OBSOLETE) Maximum distance between pairs");
+     argtable[32] = arg_file0(" ", " ", NULL, " ");
+     argtable[33] = arg_int0(NULL, " ", NULL, " ");
+     argtable[34] = arg_int0(NULL, " ", NULL, " ");
+     argtable[35] = arg_int0(NULL, " ", NULL, " ");
      argtable[36] = arg_int0(NULL, "report-n-best", NULL, "Report the <n> best alignments");
      argtable[37] = arg_int0(NULL, "report-n-hits", NULL, "Report <n> hits");
      argtable[38] = arg_int0(NULL, "num-seeds", NULL, "Number of seeds per read");
      argtable[39] = arg_int0(NULL, "min-num-seeds", NULL, "Minimum number of seeds to create a CAL (if -1, the maxixum will be taken)");
-     argtable[40] = arg_lit0(NULL, "gpu-enable", "(OBSOLETE) Enable GPU Process");
-     argtable[41] = arg_lit0(NULL, "report-only-paired", "(OBSOLETE) Report only the paired reads");
+     argtable[40] = arg_lit0(NULL, " ", " ");
+     argtable[41] = arg_lit0(NULL, " ", " ");
      argtable[42] = arg_int0(NULL, "filter-read-mappings", NULL, "Reads that map in more than <n> locations are discarded");
      argtable[43] = arg_int0(NULL, "filter-seed-mappings", NULL, "Seeds that map in more than <n> locations are discarded");
      argtable[44] = arg_lit0(NULL, "report-best", "Report all alignments with best score");

src/sw_server.c

@@ -620,13 +620,8 @@ void apply_sw_bs_4nt(sw_server_input_t* input, batch_t *batch) {
 
   alignment_t *alignment;
   array_list_t *alignment_list;
-
-  // Kept for legacy reasons, using the tag object list now
-  // Should be refactored in the future
-  char *optional_fields = NULL;
-  int optional_fields_length = 100;
-
   array_list_t **mapping_lists;
+
   size_t num_targets;
   size_t *targets;
 
@@ -706,14 +701,14 @@ void apply_sw_bs_4nt(sw_server_input_t* input, batch_t *batch) {
                   strdup(new_cigar_code_string(cigar_code)), 
                   cigar_code_get_num_ops(cigar_code), 
                   norm_score * 254, 1, (num_cals > 1),
-                  optional_fields_length, optional_fields, alignment);
+                  0, NULL, alignment);
 
-          // set optional fields
+          // Set optional fields
           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);
 
-          bam_int_t AS = (bam_int_t) norm_score * 100;
+          bam_int_t AS = (bam_int_t) (norm_score * 100.0);
           bam_int_t NH = num_cals;
           bam_int_t NM = cigar_code->distance;