X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam_view.c;h=528309897bbf7c2a35bb4f2fa4727f522afb889e;hb=3a1bd4d97b4d58148b5a7fd845a3b6a023eecbed;hp=402e280606f7551dfdcc1667dcb289dc78c41a4e;hpb=17d567123ba07d6c41a840ce94c1f21c6c3c2a7f;p=samtools.git

diff --git a/sam_view.c b/sam_view.c
index 402e280..5283098 100644
--- a/sam_view.c
+++ b/sam_view.c
@@ -14,14 +14,14 @@ KHASH_SET_INIT_STR(rg)
 // data passed to the bam_fetch callback is encapsulated in this struct.
 typedef struct {
 	bam_header_t *header;
-	int *count;
+	int64_t *count;  // int does overflow for very big BAMs
 } count_func_data_t;
 
 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))))
@@ -120,13 +128,13 @@ int main_samview(int argc, char *argv[])
 {
 	int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0;
 	int of_type = BAM_OFDEC, is_long_help = 0, n_threads = 0;
-	int count = 0;
+	int64_t count = 0;
 	samfile_t *in = 0, *out = 0;
 	char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0, *q;
 
 	/* 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;
@@ -265,7 +274,7 @@ int main_samview(int argc, char *argv[])
 
 view_end:
 	if (is_count && ret == 0) {
-		printf("%d\n", count);
+		printf("%ld\n", count); // compilers on some platforms may complain about printing int64_t with %ld
 	}
 	// close files, free and return
 	free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);