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Fix bam IO to take account of BAM_FPAIRED when checking BAM_FREAD1/2 #18

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Fix bam IO to take account of BAM_FPAIRED when checking BAM_FREAD1/2 #18

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6 changes: 3 additions & 3 deletions bwaseqio.c
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Original file line number Diff line number Diff line change
Expand Up @@ -104,9 +104,9 @@ static bwa_seq_t *bwa_read_bam(bwa_seqio_t *bs, int n_needed, int *n, int is_com
while ((res = bam_read1(bs->fp, b)) >= 0) {
uint8_t *s, *q;
int go = 0;
if ((bs->which & 1) && (b->core.flag & BAM_FREAD1)) go = 1;
if ((bs->which & 2) && (b->core.flag & BAM_FREAD2)) go = 1;
if ((bs->which & 4) && !(b->core.flag& BAM_FREAD1) && !(b->core.flag& BAM_FREAD2))go = 1;
if ((bs->which & 1) && ((b->core.flag&(BAM_FPAIRED|BAM_FREAD1)) == (BAM_FPAIRED|BAM_FREAD1))) go = 1;
if ((bs->which & 2) && ((b->core.flag&(BAM_FPAIRED|BAM_FREAD2)) == (BAM_FPAIRED|BAM_FREAD2))) go = 1;
if ((bs->which & 4) && ((b->core.flag&(BAM_FPAIRED|BAM_FREAD1)) != (BAM_FPAIRED|BAM_FREAD1)) && ((b->core.flag&(BAM_FPAIRED|BAM_FREAD2)) != (BAM_FPAIRED|BAM_FREAD2)))go = 1;
if (go == 0) continue;
l = b->core.l_qseq;
p = &seqs[n_seqs++];
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