From fbb4b1356096b31bb5f1956f864f4c76b21565f6 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 24 Mar 2012 17:32:45 -0400 Subject: [PATCH] filter on query sequence length (not aln len) --- sam_view.c | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/sam_view.c b/sam_view.c index 402e280..c7a4774 100644 --- a/sam_view.c +++ b/sam_view.c @@ -21,7 +21,7 @@ typedef khash_t(rg) *rghash_t; // FIXME: we'd better use no global variables... static rghash_t g_rghash = 0; -static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0, g_qual_scale = 0; +static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0, g_qual_scale = 0, g_min_qlen = 0; static uint32_t g_subsam_seed = 0; static double g_subsam_frac = -1.; static char *g_library, *g_rg; @@ -41,6 +41,14 @@ static int process_aln(const bam_header_t *h, bam1_t *b) qual[i] = c < 93? c : 93; } } + if (g_min_qlen > 0) { + int k, qlen = 0; + uint32_t *cigar = bam1_cigar(b); + for (k = 0; k < b->core.n_cigar; ++k) + if ((bam_cigar_type(bam_cigar_op(cigar[k]))&1) || bam_cigar_op(cigar[k]) == BAM_CHARD_CLIP) + qlen += bam_cigar_oplen(cigar[k]); + if (qlen < g_min_qlen) return 1; + } if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off)) return 1; if (g_bed && b->core.tid >= 0 && !bed_overlap(g_bed, h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b)))) @@ -126,7 +134,7 @@ int main_samview(int argc, char *argv[]) /* parse command-line options */ strcpy(in_mode, "r"); strcpy(out_mode, "w"); - while ((c = getopt(argc, argv, "SbBct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:Q:@:")) >= 0) { + while ((c = getopt(argc, argv, "SbBct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:Q:@:m:")) >= 0) { switch (c) { case 's': if ((g_subsam_seed = strtol(optarg, &q, 10)) != 0) { @@ -135,6 +143,7 @@ int main_samview(int argc, char *argv[]) } g_subsam_frac = strtod(q, &q); break; + case 'm': g_min_qlen = atoi(optarg); break; case 'c': is_count = 1; break; case 'S': is_bamin = 0; break; case 'b': is_bamout = 1; break; -- 2.39.2