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[samtools.git] / bam2depth.c

diff --git a/bam2depth.c b/bam2depth.c
index 95588f96b5a4ebc1a531bc11bb5c2c43183bf08d..87a4c5b6cf379c026c6883d95a44c700cc3d5364 100644 (file)
--- a/bam2depth.c
+++ b/bam2depth.c
@@ -13,6 +13,7 @@
 typedef struct {     // auxiliary data structure
        bamFile fp;      // the file handler
        bam_iter_t iter; // NULL if a region not specified
+       int min_mapQ, min_len; // mapQ filter; length filter
 } aux_t;
 
 void *bed_read(const char *fn); // read a BED or position list file
@@ -20,10 +21,15 @@ void bed_destroy(void *_h);     // destroy the BED data structure
 int bed_overlap(const void *_h, const char *chr, int beg, int end); // test if chr:beg-end overlaps
 
 // This function reads a BAM alignment from one BAM file.
-static int read_bam(void *data, bam1_t *b)
+static int read_bam(void *data, bam1_t *b) // read level filters better go here to avoid pileup
 {
        aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure
-       return aux->iter? bam_iter_read(aux->fp, aux->iter, b) : bam_read1(aux->fp, b);
+       int ret = aux->iter? bam_iter_read(aux->fp, aux->iter, b) : bam_read1(aux->fp, b);
+       if (!(b->core.flag&BAM_FUNMAP)) {
+               if ((int)b->core.qual < aux->min_mapQ) b->core.flag |= BAM_FUNMAP;
+               else if (aux->min_len && bam_cigar2qlen(&b->core, bam1_cigar(b)) < aux->min_len) b->core.flag |= BAM_FUNMAP;
+       }
+       return ret;
 }
 
 #ifdef _MAIN_BAM2DEPTH
@@ -32,7 +38,7 @@ int main(int argc, char *argv[])
 int main_depth(int argc, char *argv[])
 #endif
 {
-       int i, n, tid, beg, end, pos, *n_plp, baseQ = 0;
+       int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0, min_len = 0;
        const bam_pileup1_t **plp;
        char *reg = 0; // specified region
        void *bed = 0; // BED data structure
@@ -41,29 +47,33 @@ int main_depth(int argc, char *argv[])
        bam_mplp_t mplp;
 
        // parse the command line
-       while ((n = getopt(argc, argv, "r:b:q:")) >= 0) {
+       while ((n = getopt(argc, argv, "r:b:q:Q:l:")) >= 0) {
                switch (n) {
+                       case 'l': min_len = atoi(optarg); break; // minimum query length
                        case 'r': reg = strdup(optarg); break;   // parsing a region requires a BAM header
                        case 'b': bed = bed_read(optarg); break; // BED or position list file can be parsed now
                        case 'q': baseQ = atoi(optarg); break;   // base quality threshold
+                       case 'Q': mapQ = atoi(optarg); break;    // mapping quality threshold
                }
        }
        if (optind == argc) {
-               fprintf(stderr, "Usage: bam2depth [-r reg] [-q baseQthres] [-b in.bed] <in1.bam> [...]\n");
+               fprintf(stderr, "Usage: bam2depth [-r reg] [-q baseQthres] [-Q mapQthres] [-l minQLen] [-b in.bed] <in1.bam> [...]\n");
                return 1;
        }
 
        // initialize the auxiliary data structures
        n = argc - optind; // the number of BAMs on the command line
-       data = calloc(n, sizeof(void*));
-       beg = 0; end = 1<<30; tid = -1;
+       data = calloc(n, sizeof(void*)); // data[i] for the i-th input
+       beg = 0; end = 1<<30; tid = -1;  // set the default region
        for (i = 0; i < n; ++i) {
                bam_header_t *htmp;
                data[i] = calloc(1, sizeof(aux_t));
                data[i]->fp = bam_open(argv[optind+i], "r"); // open BAM
+               data[i]->min_mapQ = mapQ;                    // set the mapQ filter
+               data[i]->min_len  = min_len;                 // set the qlen filter
                htmp = bam_header_read(data[i]->fp);         // read the BAM header
                if (i == 0) {
-                       h = htmp; // keep the header for the 1st BAM
+                       h = htmp; // keep the header of the 1st BAM
                        if (reg) bam_parse_region(h, reg, &tid, &beg, &end); // also parse the region
                } else bam_header_destroy(htmp); // if not the 1st BAM, trash the header
                if (tid >= 0) { // if a region is specified and parsed successfully
@@ -80,15 +90,15 @@ int main_depth(int argc, char *argv[])
        while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position
                if (pos < beg || pos >= end) continue; // out of range; skip
                if (bed && bed_overlap(bed, h->target_name[tid], pos, pos + 1) == 0) continue; // not in BED; skip
-               fputs(h->target_name[tid], stdout); printf("\t%d", pos+1);
-               for (i = 0; i < n; ++i) {
+               fputs(h->target_name[tid], stdout); printf("\t%d", pos+1); // a customized printf() would be faster
+               for (i = 0; i < n; ++i) { // base level filters have to go here
                        int j, m = 0;
                        for (j = 0; j < n_plp[i]; ++j) {
                                const bam_pileup1_t *p = plp[i] + j; // DON'T modfity plp[][] unless you really know
                                if (p->is_del || p->is_refskip) ++m; // having dels or refskips at tid:pos
                                else if (bam1_qual(p->b)[p->qpos] < baseQ) ++m; // low base quality
                        }
-                       printf("\t%d", n_plp[i] - m);
+                       printf("\t%d", n_plp[i] - m); // this the depth to output
                }
                putchar('\n');
        }