Merge branch 'hotfix/0.4.2'

cancerit · Apr 3, 2017 · 7b24543 · 7b24543
2 parents 789bce0 + ef836f6
commit 7b24543
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Showing 9 changed files with 27 additions and 29 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,6 @@
+### 0.4.1
+* Modified parsing of regions to enable names with : in (i.e. GRCh38)
+
 ### 0.4.1
 * Updated libBigWig to 0.3.1 - fixes issue with overflow in very large zoom levels
 

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-0.4.1
+0.4.2
diff --git a/c/Makefile b/c/Makefile
@@ -85,7 +85,7 @@ make_BW=../bin/makebw
 
 .NOTPARALLEL: test
 
-all: clean pre make_htslib_tmp $(BAM2BG_TARGET) $(BAM2BW_TARGET) $(BAM2BASES_TARGET) remove_htslib_tmp $(JOIN_TARGET) $(CAT_TARGET) $(BG2BW_TARGET) $(DEXDEPTH_TARGET) test
+all: clean pre make_htslib_tmp $(BAM2BG_TARGET) $(BAM2BW_TARGET) $(BAM2BASES_TARGET) $(JOIN_TARGET) $(CAT_TARGET) $(BG2BW_TARGET) $(DEXDEPTH_TARGET) remove_htslib_tmp test
 	@echo  bwcat, bwjoin, bam2bedgraph, bam2bw, detectExtremeDepth and bam2bwbases compiled.
 
 $(CAT_TARGET): $(OBJS)

diff --git a/c/bam2bw.c b/c/bam2bw.c
@@ -219,16 +219,6 @@ bigWigFile_t *initialise_bw_output(char *out_file, chromList_t *chromList){
   return NULL;
 }
 
-char *get_contig_from_region(char *region){
-  int beg = 0;
-  int end = 0;
-  const char *q = hts_parse_reg(region, &beg, &end);
-  char *tmp = (char*)malloc(q - region + 1);
-  strncpy(tmp, region, q - region);
-  tmp[q - region] = 0;
-  return tmp;
-}
-
 uint32_t getContigLength(char *contig,chromList_t *chromList){
   int i=0;
   for(i=0;i<chromList->nKeys;i++){
@@ -351,8 +341,7 @@ int main(int argc, char *argv[]){
 	  if(include_zeroes == 1){
 	    uint32_t reg_start;
 	    uint32_t reg_stop;
-	    char *contig = malloc(sizeof(char) * 2048);
-	    parseRegionString(our_region_list[i], contig, &reg_start, &reg_stop);
+	    char *contig = parseRegionString(our_region_list[i], &reg_start, &reg_stop);
 	    uint32_t len = getContigLength(contig,chromList);
 	    check(len != -1,"Error fetching length of contig %s.",contig);
 	    //Append end of chromosome if zeroes

diff --git a/c/bam2bwbases.c b/c/bam2bwbases.c
@@ -346,10 +346,10 @@ int main(int argc, char *argv[]){
   int chck = 0;
   uint32_t sta;
 	uint32_t sto;
-	char *contig = malloc(sizeof(char) * 2048);
+	char *contig;
   int i=0;
 	for(i=0;i<no_of_regions;i++){
-	  parseRegionString(our_region_list[i], contig, &sta, &sto);
+	  contig = parseRegionString(our_region_list[i], &sta, &sto);
 	  int k=0;
     for(k=0;k<4;k++){
       perbase[k].reg_start = sta;
@@ -375,6 +375,7 @@ int main(int argc, char *argv[]){
         check(chck==0,"Error adding region to bw '%s:%"PRIu32"-%"PRIu32"\t%f'. TID: %d\tErrno: %d",perbase[b].head->target_name[perbase[b].ltid],start,stop,result,perbase[b].ltid,chck);
       }
     }
+    free(contig);
     bam_hdr_destroy(perbase[0].head);
 	}
 

diff --git a/c/bam_access.c b/c/bam_access.c
@@ -237,8 +237,7 @@ int process_bam_region_bases(char *input_file, bw_func_reg perbase_pileup_func,
   uint32_t last_pos = 0;
   uint32_t start;
   uint32_t stop;
-  char *contig = malloc(sizeof(char) * 2048);
-  parseRegionString(region, contig, &start, &stop);
+  char *contig = parseRegionString(region, &start, &stop);
   int x=0;
   for(x=0;x<4;x++){
     perbase[x].idx = idx;
@@ -338,8 +337,7 @@ int process_bam_region(char *input_file, bw_func_reg pileup_func, tmpstruct_t *t
   uint32_t last_pos = 0;
   uint32_t reg_sta;
   uint32_t reg_sto;
-  char *contig = malloc(sizeof(char) * 2048);
-  parseRegionString(region, contig, &reg_sta, &reg_sto);
+  char *contig = parseRegionString(region, &reg_sta, &reg_sto);
   if(reg_sta>1){
    tmp->lstart=reg_sta-1;
    tmp->lpos=reg_sta-1;

diff --git a/c/catbw.c b/c/catbw.c
@@ -137,10 +137,11 @@ int main(int argc, char *argv[]){
 
   if(region!=NULL){
     //Check and parse region
-    char contig[1024]= "";
-    uint32_t start,stop;
-    int chk = parseRegionString(region,contig,&start,&stop);
-    check(chk>0,"Error parsing region string '%s'",region);
+    uint32_t start = 0;
+    uint32_t stop = 0;
+    char *contig = NULL;
+    contig = parseRegionString(region,&start,&stop);
+    check(contig!=NULL,"Error parsing region string '%s'",region);
     //retrieve region intervals
     //intervals = bwGetValues(fp, contig, start, stop, inc_na);
     intervals = bwGetOverlappingIntervals(fp, contig, start-1, stop);
@@ -149,10 +150,12 @@ int main(int argc, char *argv[]){
       uint32_t j=0;
       for(j=0;j<intervals->l;j++){
         //print interval
+        fprintf(stderr,"***INTERVAL****\t%s:%d-%d\n",contig,(intervals->start)[j],(intervals->end)[j]);
         fprintf(out,out_pattern,contig,(intervals->start)[j],(intervals->end)[j],(intervals->value)[j]);
       }
       bwDestroyOverlappingIntervals(intervals);
     }
+    free(contig);
   }else{
     //No region so iterate through each contig listed in the header file
     //Read in the list of chromosomes

diff --git a/c/utils.c b/c/utils.c
@@ -33,6 +33,7 @@
 #include <stdlib.h>
 #include <alloca.h>
 #include <inttypes.h>
+#include "htslib/sam.h"
 #include "utils.h"
 
 
@@ -98,8 +99,11 @@ int line_count (char *file_path){
   return -1;
 }
 
-int parseRegionString(char *region, char *contig, uint32_t *start, uint32_t *stop){
-  int check_parse = sscanf(region,region_format,contig,start,stop);
-  if(check_parse != 3) return 0;
-  return check_parse;
+int parseRegionString(char *region, uint32_t *start, uint32_t *stop){
+  const char *q = hts_parse_reg(region, start, stop);
+  char *contig = (char*)malloc(q - region + 1);
+  strncpy(contig, region, q - region);
+  contig[q - region] = 0;
+  *start = *start+1;
+  return contig;
 }
diff --git a/c/utils.h b/c/utils.h
@@ -44,6 +44,6 @@ int check_exist(char *fname);
 
 int parse_file_name( char *dir, char *fname, const char *file);
 
-int parseRegionString(char *region, char *contig, uint32_t *start, uint32_t *stop);
+int parseRegionString(char *region, uint32_t *start, uint32_t *stop);
 
 #endif