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Remove the mpileup BAM_CREF_SKIP filter. #2281

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Remove the mpileup BAM_CREF_SKIP filter. #2281

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11 changes: 1 addition & 10 deletions bam2bcf_edlib.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1559,19 +1559,10 @@ int bcf_edlib_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos,
}
}

int qbeg, qpos, qend, tbeg, tend, kk;
int qbeg, qpos, qend, tbeg, tend;
uint8_t *seq = bam_get_seq(p->b);
uint32_t *cigar = bam_get_cigar(p->b);
if (p->b->core.flag & BAM_FUNMAP) continue;

// FIXME: the following loop should be better moved outside;
// nonetheless, realignment should be much slower anyway.
for (kk = 0; kk < p->b->core.n_cigar; ++kk)
if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP)
break;
if (kk < p->b->core.n_cigar)
continue;

// determine the start and end of sequences for alignment
int left2 = left, right2 = right;
int min_win_size = MAX(-biggest_del, biggest_ins);
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11 changes: 1 addition & 10 deletions bam2bcf_indel.c
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Original file line number Diff line number Diff line change
Expand Up @@ -845,19 +845,10 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos,
}
}

int qbeg, qpos, qend, tbeg, tend, kk;
int qbeg, qpos, qend, tbeg, tend;
uint8_t *seq = bam_get_seq(p->b);
uint32_t *cigar = bam_get_cigar(p->b);
if (p->b->core.flag & BAM_FUNMAP) continue;

// FIXME: the following loop should be better moved outside;
// nonetheless, realignment should be much slower anyway.
for (kk = 0; kk < p->b->core.n_cigar; ++kk)
if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP)
break;
if (kk < p->b->core.n_cigar)
continue;

// determine the start and end of sequences for alignment
// FIXME: loops over CIGAR multiple times
int left2 = left, right2 = right;
Expand Down