Merge pull request #96 from dpryan79/issue83

dpryan79 · May 23, 2020 · 59df03c · 59df03c
2 parents f331162 + dfa5206
commit 59df03c
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Showing 4 changed files with 10 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,7 @@
+Version 0.5.1:
+
+   * Fixed an issue in `MethylDackel mbias` due to an uninitialized value (issue #93).
+
 Version 0.5.0:
 
    * Fixed an issue with the `--cytosine_report` option where the reported chromosome name could be wrong IF the input BAM files were very sparse and multiple threads were used. (issue #88)

diff --git a/MBias.c b/MBias.c
@@ -58,7 +58,7 @@ void *extractMBias(void *foo) {
     Config *config = (Config*) foo;
     bam_hdr_t *hdr;
     bam_mplp_t iter;
-    int ret, tid, pos, i, seqlen, rv, o = 0;
+    int ret, tid, pos = 0, i, seqlen, rv, o = 0;
     int32_t bedIdx = 0;
     int strand;
     int n_plp; //This will need to be modified for multiple input files
@@ -301,6 +301,7 @@ int mbias_main(int argc, char *argv[]) {
     config.keepCpG = 1; config.keepCHG = 0; config.keepCHH = 0;
     config.minMapq = 10; config.minPhred = 5; config.keepDupes = 0;
     config.keepSingleton = 0, config.keepDiscordant = 0;
+    config.filterMappability = 0;
 
     config.fp = NULL;
     config.bai = NULL;

diff --git a/Makefile b/Makefile
@@ -11,7 +11,7 @@ CFLAGS ?= -Wall -g -O3 -pthread
 all: MethylDackel
 
 OBJS = common.o bed.o svg.o pileup.o extract.o MBias.o mergeContext.o perRead.o
-VERSION = 0.5.0
+VERSION = 0.5.1
 
 version.h:
 	echo '#define VERSION "$(VERSION)"' > $@

diff --git a/common.c b/common.c
@@ -47,6 +47,7 @@ void print_version() {
 }
 
 inline int isCpG(char *seq, int pos, int seqlen) {
+    if(pos >= seqlen) return 0;
     if(*(seq+pos) == 'C' || *(seq+pos) == 'c') {
         if(pos+1 == seqlen) return 0;
         if(*(seq+pos+1) == 'G' || *(seq+pos+1) == 'g') return 1;
@@ -60,6 +61,7 @@ inline int isCpG(char *seq, int pos, int seqlen) {
 }
 
 inline int isCHG(char *seq, int pos, int seqlen) {
+    if(pos >= seqlen) return 0;
     if(*(seq+pos) == 'C' || *(seq+pos) == 'c') {
         if(pos+2 >= seqlen) return 0;
         if(*(seq+pos+2) == 'G' || *(seq+pos+2) == 'g') return 1;
@@ -73,6 +75,7 @@ inline int isCHG(char *seq, int pos, int seqlen) {
 }
 
 inline int isCHH(char *seq, int pos, int seqlen) {
+    if(pos >= seqlen) return 0;
     if(*(seq+pos) == 'C' || *(seq+pos) == 'c') return 1;
     else if(*(seq+pos) == 'G' || *(seq+pos) == 'g') return -1;
     return 0;