Opened 8 years ago

Closed 8 years ago

#810 closed defect (fixed)

Bam::end() doesn't work when cigar contains BAM_CEQUAL and BAM_CDIFF

Reported by: Peter Owned by: Peter
Priority: major Milestone: yat 0.12.1
Component: omic Version: 0.12
Keywords: Cc:

Description

Bam::end(void) is implemented using bam_calend, but that function doesn't work when the cigar contains BAM_CEQUAL or BAM_CDIFF. I'd consider this simply a bug in libbbam.

I propose we check in configure if bam_calend has the bug and in that case we implement Bam::end() using our own code.

Change History (4)

comment:1 Changed 8 years ago by Peter

(In [3300]) BAM_CBACK is not #defined in older versions of bam.h. refs #810

comment:2 Changed 8 years ago by Peter

(In [3301]) refs #810. minor corrections

comment:3 Changed 8 years ago by Peter

(In [3302]) add test for BamRead::end(). Use samtools' bam_calend if HAVE_BAM_CALEND is #defined. refs #810

comment:4 Changed 8 years ago by Peter

Resolution: fixed
Status: newclosed

(In [3303]) New macro YAT_FUNC_BAM_CALEND, which checks if function bam_calend is buggy. If the function works as expected, HAVE_BAM_CALEND is AC_DEFINEd so bam_calend is used. Closes #810.

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