* added BED support to samtools view and mpileup and bcftools view

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index 170bd843608b99aec35161141ee6afaad848db5e..fbffdb4f178e3b11c53a735b6b062b7754844e16 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -18,10 +18,15 @@ typedef struct {
 
 typedef khash_t(rg) *rghash_t;
 
-rghash_t g_rghash = 0;
+static rghash_t g_rghash = 0;
 static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
 static char *g_library, *g_rg;
 static int g_sol2sanger_tbl[128];
+static void *g_bed;
+
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, int beg, int end);
 
 static void sol2sanger(bam1_t *b)
 {
@@ -44,6 +49,8 @@ static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
 {
        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))))
+               return 1;
        if (g_rg || g_rghash) {
                uint8_t *s = bam_aux_get(b, "RG");
                if (s) {
@@ -90,7 +97,7 @@ int main_samview(int argc, char *argv[])
 
        /* parse command-line options */
        strcpy(in_mode, "r"); strcpy(out_mode, "w");
-       while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:CR:")) >= 0) {
+       while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:CR:L:")) >= 0) {
                switch (c) {
                case 'c': is_count = 1; break;
                case 'C': slx2sngr = 1; break;
@@ -106,6 +113,7 @@ int main_samview(int argc, char *argv[])
                case 'u': compress_level = 0; break;
                case '1': compress_level = 1; break;
                case 'l': g_library = strdup(optarg); break;
+               case 'L': g_bed = bed_read(optarg); break;
                case 'r': g_rg = strdup(optarg); break;
                case 'R': fn_rg = strdup(optarg); break;
                case 'x': of_type = BAM_OFHEX; break;
@@ -215,6 +223,7 @@ view_end:
        }
        // close files, free and return
        free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
+       if (g_bed) bed_destroy(g_bed);
        if (g_rghash) {
                khint_t k;
                for (k = 0; k < kh_end(g_rghash); ++k)
@@ -240,6 +249,7 @@ static int usage(int is_long_help)
        fprintf(stderr, "         -x       output FLAG in HEX (samtools-C specific)\n");
        fprintf(stderr, "         -X       output FLAG in string (samtools-C specific)\n");
        fprintf(stderr, "         -c       print only the count of matching records\n");
+       fprintf(stderr, "         -L FILE  output alignments overlapping the input BED FILE [null]\n");
        fprintf(stderr, "         -t FILE  list of reference names and lengths (force -S) [null]\n");
        fprintf(stderr, "         -T FILE  reference sequence file (force -S) [null]\n");
        fprintf(stderr, "         -o FILE  output file name [stdout]\n");