Fix XG handling on non-bismark/bison aligner

dpryan79 · Apr 20, 2016 · 99010c1 · 99010c1
1 parent 14ad01c
commit 99010c1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,7 @@ Version 0.1.10:
    * Added the --version/-v option.
    * Fixed the -h/--help option, which actually wasn't recognized before!
    * Added the --minDepth option.
+   * Fixed handling of the `XG` auxiliary tag, since some aligners other than bismark are using it (and for different purposes). This is the single biggest annoyance of custom auxiliary tags.
 
 Version 0.1.9:
 

diff --git a/common.c b/common.c
@@ -44,6 +44,8 @@ inline int isCHH(char *seq, int pos, int seqlen) {
 
 int getStrand(bam1_t *b) {
     char *XG = (char *) bam_aux_get(b, "XG");
+    //Only bismark uses the XG tag like this. Some other aligners use it for other purposes...
+    if(XG != NULL && *(XG+1) != 'C' && *(XG+1) != 'G') XG = NULL;
     if(XG == NULL) { //Can't handle non-directional libraries!
         if(b->core.flag & BAM_FPAIRED) {
             if((b->core.flag & 0x50) == 0x50) return 2; //Read1, reverse comp. == OB