* Merge from branches/dev/

[samtools.git] / bam_pileup.c

diff --git a/bam_pileup.c b/bam_pileup.c
index d01f9a3d56c1753d48149aef6f9325c753da6808..6a578319c24b739ea7bcfbaae7305b0f75607f52 100644 (file)
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -111,6 +111,7 @@ struct __bam_plbuf_t {
        int32_t tid, pos, max_tid, max_pos;
        int max_pu, is_eof;
        bam_pileup1_t *pu;
+       int flag_mask;
 };
 
 void bam_plbuf_reset(bam_plbuf_t *buf)
@@ -127,6 +128,12 @@ void bam_plbuf_reset(bam_plbuf_t *buf)
        buf->head = buf->tail;
 }
 
+void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask)
+{
+       if (mask < 0) buf->flag_mask = BAM_DEF_MASK;
+       else buf->flag_mask = BAM_FUNMAP | mask;
+}
+
 bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
 {
        bam_plbuf_t *buf;
@@ -136,6 +143,7 @@ bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
        buf->head = buf->tail = mp_alloc(buf->mp);
        buf->dummy = mp_alloc(buf->mp);
        buf->max_tid = buf->max_pos = -1;
+       buf->flag_mask = BAM_DEF_MASK;
        return buf;
 }
 
@@ -153,6 +161,7 @@ void bam_plbuf_destroy(bam_plbuf_t *buf)
 int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
 {
        if (b) { // fill buffer
+               if (b->core.flag & buf->flag_mask) return 0;
                bam_copy1(&buf->tail->b, b);
                buf->tail->beg = b->core.pos; buf->tail->end = bam_calend(&b->core, bam1_cigar(b));
                if (!(b->core.tid >= buf->max_tid || (b->core.tid == buf->max_tid && buf->tail->beg >= buf->max_pos))) {
@@ -197,13 +206,14 @@ int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
        return 0;
 }
 
-int bam_pileup_file(bamFile fp, bam_pileup_f func, void *func_data)
+int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data)
 {
        bam_plbuf_t *buf;
        int ret;
        bam1_t *b;
        b = (bam1_t*)calloc(1, sizeof(bam1_t));
        buf = bam_plbuf_init(func, func_data);
+       bam_plbuf_set_mask(buf, mask);
        while ((ret = bam_read1(fp, b)) >= 0)
                bam_plbuf_push(b, buf);
        bam_plbuf_push(0, buf);