Bump version

README.md

@@ -93,6 +93,8 @@ Documentation can be found at
 Changelog:
 ----------
 
+    3.3.0 Make new release for IHEC
+    3.3.0 Fix bug where conversion parameters could be ignored
     3.2.13 Fix formatting bug in mextr with multiple samples (not triggered in normal gemBS use)
     3.2.12 Ensure that conversion statistics are correctly calculated for non-stranded or reverse conversion protocols
     3.2.11 Introduce reverse_conversion option for mapping where read 1 is G2A converted and read 2 is C2T converted

gemBS/__init__.py

@@ -838,11 +838,10 @@ def prepare(self, sample, input_bam, chrom_list, output_bcf, report_file, contig
         if self.haploid:
             parameters_bscall.append('-1')
         if self.conversion != None:
-            if self.conversion.lower() == "auto":
-                if sample in self.sample_conversion:
-                    parameters_bscall.extend(['--conversion', self.sample_conversion[sample]])
-                else:
-                    parameters_bscall.extend(['--conversion', self.conversion])
+            if self.conversion.lower() == "auto" and sample in self.sample_conversion:
+                parameters_bscall.extend(['--conversion', self.sample_conversion[sample]])
+            else:
+                parameters_bscall.extend(['--conversion', self.conversion])
         if self.ref_bias != None:
             parameters_bscall.extend(['--reference-bias', self.ref_bias])
         #Thresholds

gemBS/production.py

@@ -1106,6 +1106,7 @@ def run(self,args):
                 if args.qual_threshold != None: com2.extend(['-Q',str(args.mapq_threshold)])
                 if args.right_trim != None: com2.extend(['--right-trim',str(args.right_trim)])
                 if args.left_trim != None: com2.extend(['--left-trim',str(args.left_trim)])
+                if args.conversion != None: com2.extend(['--conversion',str(args.conversion)])
                 if args.keep_duplicates != None: com2.append('-u')
                 if args.ignore_duplicates != None: com2.append('-U')
                 if args.keep_unmatched != None: com2.append('-k')

gemBS/version.py

@@ -1,4 +1,4 @@
 __VERSION_MAJOR = "3"
-__VERSION_MINOR = "2"
-__VERSION_SUBMINOR = "13"
+__VERSION_MINOR = "3"
+__VERSION_SUBMINOR = "0"
 __VERSION__ = "%s.%s.%s" % (__VERSION_MAJOR, __VERSION_MINOR,__VERSION_SUBMINOR)

tools/gemBS_plugins/compress.c

@@ -57,7 +57,7 @@ static void init_compress(void) {
 			  path = DEFAULT_PATH;
 			for (i = 0; i < COMPRESS_NONE; i++) {
 				compress_data.compress_suffix[i] = strdup(suff[i]);
-				compress_data.comp_path[i][0] = compress_data.comp_path[i][0] = NULL;
+				compress_data.comp_path[i][0] = compress_data.comp_path[i][1] = NULL;
 			}
 			int ix = 0;
 			while(pnames[ix][0] != NULL) {

tools/gemBS_plugins/mextr.c

@@ -1,7 +1,6 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <stddef.h>
-#include <locale.h>
 #include <unistd.h>
 #include <string.h>
 #include <inttypes.h>
@@ -463,11 +462,10 @@ static fmt_field_t tags[] = {
 bcf1_t *process(bcf1_t *rec)
 {
   static int idx;
-  static int32_t curr_rid = -1, prev_pos, mq[2];
+  static int32_t curr_rid = -1, prev_pos;
   static bool valid[2] = {false, false};
   static bcf1_t prev_rec;
 
-  (void)setlocale(LC_NUMERIC, "C");
   int ns = bcf_hdr_nsamples(args.hdr);
   stats_t *st = args.stats;
   if(st != NULL) st->n_sites++;
@@ -563,8 +561,6 @@ bcf1_t *process(bcf1_t *rec)
 	  }
 	}
       }
-      mq[idx] = -1;
-      if(mq_p != NULL) mq[idx] = (int32_t)(0.5 + sqrt(ms_mq / (double)tot_n));
       valid[idx] = true;
       // Here is the logic for deciding what we print
       if(rec->rid != curr_rid) curr_rid = rec->rid;

tools/gemBS_plugins/output.c

@@ -178,7 +178,6 @@ void output_cpg(args_t *args, bcf1_t *rec, fmt_field_t *tags, gt_meth *sample_gt
 	double z = 0.0;
 	gt_meth *g = sample_gt[idx ^ pos] + ix;
 	if(!g->skip) {
-	  double m = get_meth(g, pos);
 	  if(!pos) {
 	    if(g->counts[5] >= args->min_nc && (g->counts[5] + g->counts[7] >= args->min_inform)) {
 	      if(args->sel_mode == SELECT_HOM) z = exp(g->gt_prob[4]);
@@ -260,8 +259,9 @@ static char *rgb_tab[11] = { "0,255,0", "55,255,0", "105,255,0", "155,255,0", "2
 
 void output_bedmethyl(args_t *args, bcf1_t *rec, fmt_field_t *tags, gt_meth *sample_gt[], int idx) {
   static char *cx;
-  static int32_t cx_n,old_rid = 0xffffffff;
+  static int32_t cx_n,old_rid = 0xffffffff, old_pos = -1;
 
+  if(rec->rid == old_rid && rec->pos <= old_pos) return;
   int ns = bcf_hdr_nsamples(args->hdr);
   if(ns > 1) return;
   gt_meth *g = sample_gt[idx];
@@ -310,7 +310,6 @@ void output_bedmethyl(args_t *args, bcf1_t *rec, fmt_field_t *tags, gt_meth *sam
       FILE *fp = args->wigfile;
       if(fp != NULL) {
 	if(rec->rid != old_rid) {
-	  old_rid = rec->rid;
 	  fprintf(fp, "variableStep chrom=%s\n", args->hdr->id[BCF_DT_CTG][rec->rid].key);
 	}
 	fprintf(fp, "%u\t%.4g\n", rec->pos + 1, 100.0 * m);
@@ -323,5 +322,7 @@ void output_bedmethyl(args_t *args, bcf1_t *rec, fmt_field_t *tags, gt_meth *sam
 	      args->hdr->id[BCF_DT_CTG][rec->rid].key, rec->pos, rec->pos + 1, args->bedmethyl_desc, cov > 1000 ? 1000 : cov, strand, 
 	      rec->pos, rec->pos + 1, rgb_tab[(int)(m * 10.0 + 0.5)], cov, (int)(100.0 * m), rtmp, rtmp + 4, gq);
     }
+    old_rid = rec->rid;
+    old_pos = rec->pos;
   }
 }