* samtools-0.1.3-12 (r259)

 * use the new I/O interface in pileup

diff --git a/bam.h b/bam.h
index 1195e75be3220a0ecfe569de249dc1a5a70780a5..7167dc155588642ea79ce30b282b0e4dd84c0cef 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -512,17 +512,6 @@ extern "C" {
         */
        int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
 
-       /*!
-         @abstract         A more convenient interface to bam_plbuf_push()
-         @param  fp        BAM file handler
-         @param  func      user defined function
-         @param  func_data user provided data
-
-         @discussion The file position indicator must be placed right
-         before the start of an alignment. See also bam_plbuf_push().
-        */
-       int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
-
        struct __bam_lplbuf_t;
        typedef struct __bam_lplbuf_t bam_lplbuf_t;
 

diff --git a/bam_pileup.c b/bam_pileup.c
index 616767a932b16222c1af7bdd3c5752124ebdfb0d..46906dba429032c49920f61a4149c29ec43eae11 100644 (file)
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -1,7 +1,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <ctype.h>
-#include "bam.h"
+#include "sam.h"
 
 typedef struct __linkbuf_t {
        bam1_t b;
@@ -206,19 +206,3 @@ int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
        }
        return 0;
 }
-
-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);
-       bam_plbuf_destroy(buf);
-       free(b->data); free(b);
-       return 0;
-}

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 46a2b9957997f89645bd2cae1c80298ee9ef8b28..23e0dd00a5eda44bbc337a17b1692adc1ecb3b8c 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -1,7 +1,7 @@
 #include <stdio.h>
 #include <unistd.h>
 #include <ctype.h>
-#include "bam.h"
+#include "sam.h"
 #include "faidx.h"
 #include "bam_maqcns.h"
 #include "khash.h"
@@ -26,7 +26,7 @@ typedef struct {
        int tid, len, last_pos;
        int mask;
        char *ref;
-       glfFile fp; // for glf output only
+       glfFile fp_glf; // for glf output only
 } pu_data_t;
 
 char **__bam_get_lines(const char *fn, int *_n);
@@ -103,9 +103,9 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
        if (d->fai && (int)tid != d->tid) {
                if (d->ref) { // then write the end mark
                        g3->rtype = GLF3_RTYPE_END;
-                       glf3_write1(d->fp, g3);
+                       glf3_write1(d->fp_glf, g3);
                }
-               glf3_ref_write(d->fp, d->h->target_name[tid], d->h->target_len[tid]); // write reference
+               glf3_ref_write(d->fp_glf, d->h->target_name[tid], d->h->target_len[tid]); // write reference
                free(d->ref);
                d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len);
                d->tid = tid;
@@ -117,7 +117,7 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
        g3->rtype = GLF3_RTYPE_SUB;
        g3->offset = pos - d->last_pos;
        d->last_pos = pos;
-       glf3_write1(d->fp, g3);
+       glf3_write1(d->fp_glf, g3);
        if (proposed_indels)
                r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
        else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0);
@@ -139,7 +139,7 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
                g3->max_len = (abs(r->indel1) > abs(r->indel2)? abs(r->indel1) : abs(r->indel2)) + 1;
                g3->indel_seq[0] = strdup(r->s[0]+1);
                g3->indel_seq[1] = strdup(r->s[1]+1);
-               glf3_write1(d->fp, g3);
+               glf3_write1(d->fp_glf, g3);
                bam_maqindel_ret_destroy(r);
        }
        free(g);
@@ -291,54 +291,38 @@ int bam_pileup(int argc, char *argv[])
                return 1;
        }
        if (fn_fa) d->fai = fai_load(fn_fa);
-       free(fn_fa);
-       if (d->format & (BAM_PLF_CNS|BAM_PLF_GLF)) bam_maqcns_prepare(d->c);
-       if (d->format & BAM_PLF_GLF) {
+       if (d->format & (BAM_PLF_CNS|BAM_PLF_GLF)) bam_maqcns_prepare(d->c); // consensus calling
+       if (d->format & BAM_PLF_GLF) { // for glf output
                glf3_header_t *h;
                h = glf3_header_init();
-               d->fp = bgzf_fdopen(fileno(stdout), "w");
-               glf3_header_write(d->fp, h);
+               d->fp_glf = bgzf_fdopen(fileno(stdout), "w");
+               glf3_header_write(d->fp_glf, h);
                glf3_header_destroy(h);
        }
        if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)))
                fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n");
-       if (fn_list) { // the input is SAM
-               tamFile fp;
-               bam1_t *b;
-               int ret;
-               bam_plbuf_t *buf = bam_plbuf_init(pileup_func, d);
-               bam_plbuf_set_mask(buf, d->mask);
-               d->h = sam_header_read2(fn_list);
-               if (fn_pos) d->hash = load_pos(fn_pos, d->h);
-               fp = sam_open(argv[optind]);
-               b = (bam1_t*)calloc(1, sizeof(bam1_t));
-               while ((ret = sam_read1(fp, d->h, b)) >= 0)
-                       bam_plbuf_push(b, buf);
-               bam_plbuf_push(0, buf);
-               bam_plbuf_destroy(buf);
-               bam_destroy1(b);
-               sam_close(fp);
-       } else { // the input is BAM
-               bamFile fp;
-               fp = (strcmp(argv[optind], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[optind], "r");
-               d->h = bam_header_read(fp);
-               if (d->h == 0) {
+       {
+               samfile_t *fp;
+               fp = fn_list? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);
+               if (fp->header == 0) {
                        fprintf(stderr, "[bam_pileup] fail to read the BAM header. Abort!\n");
                        return 1;
                }
+               d->h = fp->header;
                if (fn_pos) d->hash = load_pos(fn_pos, d->h);
-               bam_pileup_file(fp, d->mask, pileup_func, d);
-               bam_close(fp);
+               sampileup(fp, d->mask, pileup_func, d);
+               samclose(fp); // d->h will be destroyed here
        }
-       if (d->format & BAM_PLF_GLF) bgzf_close(d->fp);
+
+       // free
+       if (d->format & BAM_PLF_GLF) bgzf_close(d->fp_glf);
        if (fn_pos) { // free the hash table
                khint_t k;
                for (k = kh_begin(d->hash); k < kh_end(d->hash); ++k)
                        if (kh_exist(d->hash, k)) free(kh_val(d->hash, k));
                kh_destroy(64, d->hash);
        }
-       free(fn_pos); free(fn_list);
-       bam_header_destroy(d->h);
+       free(fn_pos); free(fn_list); free(fn_fa);
        if (d->fai) fai_destroy(d->fai);
        bam_maqcns_destroy(d->c);
        free(d->ido); free(d->ref); free(d);

diff --git a/bamtk.c b/bamtk.c
index a7e75cb59c9820201fd670fe0f570819acb7117f..2125ee4ea50b6c5b38cf286dad308124bbbc856f 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.3-11 (r258)"
+#define PACKAGE_VERSION "0.1.3-12 (r259)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/sam.c b/sam.c
index a13327482614940078982ba3ec3ed2fd0d342647..85343398a8d5356a7ce1343970653adb5204a652 100644 (file)
--- a/sam.c
+++ b/sam.c
@@ -138,3 +138,19 @@ int samwrite(samfile_t *fp, const bam1_t *b)
                return l + 1;
        }
 }
+
+int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
+{
+       bam_plbuf_t *buf;
+       int ret;
+       bam1_t *b;
+       b = bam_init1();
+       buf = bam_plbuf_init(func, func_data);
+       bam_plbuf_set_mask(buf, mask);
+       while ((ret = samread(fp, b)) >= 0)
+               bam_plbuf_push(b, buf);
+       bam_plbuf_push(0, buf);
+       bam_plbuf_destroy(buf);
+       bam_destroy1(b);
+       return 0;
+}

diff --git a/sam.h b/sam.h
index 1e50550150648b7190fed98c22cddc0daa6ecda8..93daea6834d6f6b1c6fa6874ba52219045b671a2 100644 (file)
--- a/sam.h
+++ b/sam.h
@@ -22,6 +22,7 @@ extern "C" {
        void samclose(samfile_t *fp);
        int samread(samfile_t *fp, bam1_t *b);
        int samwrite(samfile_t *fp, const bam1_t *b);
+       int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data);
 
 #ifdef __cplusplus
 }