* samtools-0.1.2-10

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 2803659aba760952d3cee687601684184390bf0e..2fe32b4909bc2fe2b9f26c143b213382c8641fe9 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -20,7 +20,7 @@ typedef struct {
        faidx_t *fai;
        khash_t(64) *hash;
        uint32_t format;
-       int tid, len;
+       int tid, len, last_pos;
        int mask;
        char *ref;
        glfFile fp; // for glf output only
@@ -58,7 +58,7 @@ static int glt_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
        bam_maqindel_ret_t *r = 0;
        int rb;
        glf1_t *g;
-       glf2_t g2;
+       glf3_t g2;
        if (d->fai == 0) {
                fprintf(stderr, "[glt_func] reference sequence is required for generating GLT. Abort!\n");
                exit(1);
@@ -66,9 +66,9 @@ static int glt_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
        if (d->hash && kh_get(64, d->hash, (uint64_t)tid<<32|pos) == kh_end(d->hash)) return 0;
        if (d->fai && (int)tid != d->tid) {
                if (d->ref) { // then write the end mark
-                       memset(&g2, 0, sizeof(glf2_t));
+                       memset(&g2, 0, sizeof(glf3_t));
                        g2.type = GLF_TYPE_END;
-                       bgzf_write(d->fp, &g2, sizeof(glf2_t));
+                       bgzf_write(d->fp, &g2, sizeof(glf3_t));
                }
                glf_ref_write(d->fp, d->h->target_name[tid]); // write reference
                free(d->ref);
@@ -79,8 +79,9 @@ static int glt_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
        g = bam_maqcns_glfgen(n, pu, bam_nt16_table[rb], d->c);
        memcpy(&g2, g, sizeof(glf1_t));
        g2.type = GLF_TYPE_NORMAL;
-       g2.pos = pos;
-       bgzf_write(d->fp, &g2, sizeof(glf2_t));
+       g2.offset = pos - d->last_pos;
+       d->last_pos = pos;
+       bgzf_write(d->fp, &g2, sizeof(glf3_t));
        r = bam_maqindel(n, pos, d->ido, pu, d->ref);
        if (r) { // then write indel line
                int g3 = 3 * n, min;
@@ -96,7 +97,7 @@ static int glt_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
                *(int16_t*)(g2.lk + 3) = (int16_t)r->indel1;
                *(int16_t*)(g2.lk + 5) = (int16_t)r->indel2;
                g2.min_lk = min < 255? min : 255;
-               bgzf_write(d->fp, &g2, sizeof(glf2_t));
+               bgzf_write(d->fp, &g2, sizeof(glf3_t));
                if (r->indel1) bgzf_write(d->fp, r->s[0]+1, r->indel1>0? r->indel1 : -r->indel1);
                if (r->indel2) bgzf_write(d->fp, r->s[1]+1, r->indel2>0? r->indel2 : -r->indel2);
                bam_maqindel_ret_destroy(r);