From 7a36e408af60d3a48eb8e2fda313f4ee748ad0fc Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 5 May 2009 13:52:25 +0000 Subject: [PATCH] * samtools-0.1.3-12 (r259) * use the new I/O interface in pileup --- bam.h | 11 ---------- bam_pileup.c | 18 +--------------- bam_plcmd.c | 58 +++++++++++++++++++--------------------------------- bamtk.c | 2 +- sam.c | 16 +++++++++++++++ sam.h | 1 + 6 files changed, 40 insertions(+), 66 deletions(-) diff --git a/bam.h b/bam.h index 1195e75..7167dc1 100644 --- 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 616767a..46906db 100644 --- a/bam_pileup.c +++ b/bam_pileup.c @@ -1,7 +1,7 @@ #include #include #include -#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 46a2b99..23e0dd0 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -1,7 +1,7 @@ #include #include #include -#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 a7e75cb..2125ee4 100644 --- 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 a133274..8534339 100644 --- 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 1e50550..93daea6 100644 --- 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 } -- 2.39.2