From fc236a11b6b6ace1cb5ee572dded25a9dec07496 Mon Sep 17 00:00:00 2001 From: peterjc Date: Fri, 30 Mar 2012 17:16:12 +0100 Subject: [PATCH] Refine logic for removing superfluous P ops (still testing ...) --- padding.c | 35 ++++++++++++++++++++++++++++------- 1 file changed, 28 insertions(+), 7 deletions(-) diff --git a/padding.c b/padding.c index 033a791..fe11da2 100644 --- a/padding.c +++ b/padding.c @@ -97,12 +97,16 @@ int bam_pad2unpad(bamFile in, bamFile out) return -1; } unpad_seq(b, &q); - if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]); - if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) { + if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) { + write_cigar(cigar2, n2, m2, cigar[0]); + } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) { write_cigar(cigar2, n2, m2, cigar[0]); if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) { write_cigar(cigar2, n2, m2, cigar[1]); } + } else { + /* Insert a dummy 0M entry to let use remove superfluous leading P ops */ + write_cigar(cigar2, n2, m2, 0); } /* Include any pads if starts with an insert */ for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k); @@ -118,17 +122,34 @@ int bam_pad2unpad(bamFile in, bamFile out) } else ++k; } write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op)); - if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]); - if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) { + if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) { + write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]); + } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) { if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) { write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]); } write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]); } - /* Remove redundant P operators between M operators, e.g. 5M2P10M -> 15M */ + /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */ + /* or right at the start before M/X/=/D */ + int pre_op, post_op; for (i = 2; i < n2; ++i) - if (bam_cigar_op(cigar2[i]) == BAM_CMATCH && bam_cigar_op(cigar2[i-1]) == BAM_CPAD && bam_cigar_op(cigar2[i-2]) == BAM_CMATCH) - cigar2[i] += cigar2[i-2], cigar2[i-2] = cigar2[i-1] = 0; + if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) { + pre_op = bam_cigar_op(cigar2[i-2]); + post_op = bam_cigar_op(cigar2[i]); + /* Note don't need to check for X/= as code above will use M only */ + if ((pre_op == BAM_CMATCH || pre_op == BAM_CDIFF || pre_op == BAM_CSOFT_CLIP || pre_op == BAM_CHARD_CLIP) || (post_op == BAM_CMATCH || post_op == BAM_CDIFF)) { + /* This is a redundant P operator */ + cigar2[i-1] = 0; // i.e. 0M + /* If had same operator either side, combine them in post_op */ + if (pre_op == post_op) { + /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/ + cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op); + cigar2[i-2] = 0; // i.e. 0M + } + } + } + /* Remove the zero'd operators (0M) */ for (i = k = 0; i < n2; ++i) if (cigar2[i]) cigar2[k++] = cigar2[i]; n2 = k; -- 2.39.2