watching the type "bam1coret" at http://samtools.sourceforge.net/samtools/bam/index.html?Functions/Functions.html#//apple_ref/c/func/bam_write1 there is the explanation of the "strand" field, which if I understand it indicates if the filament is forward or backward ... but is not implemented in the structure bam1coret. How can i get the strand field?
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TwoFaces •
two C macros are defined in "bam.h" to extract the orientation from bam1coret.flag' :
#define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
#define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
in bam.h there are BAM_FREVERSE and BAM_FMREVERSE, not bam1_strand(b) or bam1_mstrand(b)
try to grep bam1_strand in *.h
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