adding support for SAM/BAM output using htslib. Please turn on within
the Makefile.
This commit is contained in:
Nils Homer
parent
3efc33160c
commit
482a47a57e
24
Makefile
24
Makefile
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@ -2,8 +2,10 @@ CC= gcc
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#CC= clang --analyze
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CFLAGS= -g -Wall -Wno-unused-function -O2
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WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
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# set to 1 if you wish to have bam support, type 'make clean; make all'
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USE_HTSLIB=0
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AR= ar
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DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC)
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DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC)
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LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
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AOBJS= QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
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is.o bwtindex.o bwape.o kopen.o pemerge.o \
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@ -11,21 +13,33 @@ AOBJS= QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
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bwtsw2_chain.o fastmap.o bwtsw2_pair.o
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PROG= bwa
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INCLUDES=
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LIBS= -lm -lz -lpthread
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LIBS= -lm -lz -lpthread
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SUBDIRS= .
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.SUFFIXES:.c .o .cc
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.c.o:
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$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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ifeq ($(USE_HTSLIB),1)
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$(CC) -c $(CFLAGS) $(DFLAGS) -DUSE_HTSLIB $(INCLUDES) -I ../htslib $< -o $@
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else
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$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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endif
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all:$(PROG)
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bwa:libbwa.a $(AOBJS) main.o
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$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
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ifeq ($(USE_HTSLIB),1)
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$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ ../htslib/libhts.a -L. -L../htslib -lbwa $(LIBS)
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else
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$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
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endif
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bwamem-lite:libbwa.a example.o
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$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
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ifeq ($(USE_HTSLIB),1)
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$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ ../htslib/libhts.a -L. -L../htslib -lbwa $(LIBS)
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else
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$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
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endif
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libbwa.a:$(LOBJS)
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$(AR) -csru $@ $(LOBJS)
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@ -1,3 +1,4 @@
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#ifndef USE_HTSLIB
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#include <stdlib.h>
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#include <ctype.h>
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#include <string.h>
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@ -208,3 +209,4 @@ int bamlite_gzclose(gzFile file) {
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return ret;
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}
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#endif /* USE_VERBOSE_ZLIB_WRAPPERS */
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#endif
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@ -1,5 +1,6 @@
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#ifndef BAMLITE_H_
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#define BAMLITE_H_
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#ifndef USE_HTSLIB
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#include <stdint.h>
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#include <zlib.h>
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@ -112,3 +113,4 @@ extern "C" {
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#endif
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#endif
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#endif
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39
bwa.c
39
bwa.c
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@ -7,6 +7,9 @@
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#include "ksw.h"
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#include "utils.h"
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#include "kstring.h"
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#ifdef USE_HTSLIB
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#include <htslib/sam.h>
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#endif
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#ifdef USE_MALLOC_WRAPPERS
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# include "malloc_wrap.h"
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@ -274,6 +277,19 @@ void bwa_print_sam_hdr(const bntseq_t *bns, const char *rg_line)
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err_printf("%s\n", bwa_pg);
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}
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#ifdef USE_HTSLIB
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void bwa_format_sam_hdr(const bntseq_t *bns, const char *rg_line, kstring_t *str)
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{
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int i;
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extern char *bwa_pg;
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str->l = 0; str->s = 0;
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for (i = 0; i < bns->n_seqs; ++i)
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ksprintf(str, "@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
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if (rg_line) ksprintf(str, "%s\n", rg_line);
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ksprintf(str, "%s\n", bwa_pg);
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}
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#endif
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static char *bwa_escape(char *s)
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{
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char *p, *q;
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@ -319,3 +335,26 @@ err_set_rg:
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return 0;
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}
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#ifdef USE_HTSLIB
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bams_t *bams_init() {
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return calloc(1, sizeof(bams_t));
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}
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void bams_add(bams_t *bams, bam1_t *b) {
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if (bams->m == bams->l) {
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bams->m = bams->m << 2;
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bams->bams = realloc(bams->bams, sizeof(bam1_t) * bams->m);
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}
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bams->bams[bams->l] = b;
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bams->l++;
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}
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void bams_destroy(bams_t *bams) {
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int i;
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for (i = 0; i < bams->l; i++) {
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bam_destroy1(bams->bams[i]);
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}
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free(bams->bams);
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free(bams);
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}
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#endif
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32
bwa.h
32
bwa.h
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@ -4,6 +4,9 @@
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#include <stdint.h>
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#include "bntseq.h"
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#include "bwt.h"
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#ifdef USE_HTSLIB
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#include <htslib/sam.h>
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#endif
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#define BWA_IDX_BWT 0x1
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#define BWA_IDX_BNS 0x2
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@ -16,11 +19,31 @@ typedef struct {
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uint8_t *pac; // the actual 2-bit encoded reference sequences with 'N' converted to a random base
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} bwaidx_t;
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#ifdef USE_HTSLIB
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typedef struct {
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int l, m;
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bam1_t **bams;
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} bams_t;
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#endif
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typedef struct {
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int l_seq;
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#ifdef USE_HTSLIB
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char *name, *comment, *seq, *qual;
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bams_t *bams;
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#else
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char *name, *comment, *seq, *qual, *sam;
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#endif
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} bseq1_t;
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// This is here to faciliate passing around HTSLIB's bam_hdr_t structure when we are not compiling with HTSLIB
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#ifndef USE_HTSLIB
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typedef struct {
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void *ptr;
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} bam_hdr_t; // DO NOT USE
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#endif
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extern int bwa_verbose;
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extern char bwa_rg_id[256];
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@ -41,8 +64,17 @@ extern "C" {
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void bwa_idx_destroy(bwaidx_t *idx);
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void bwa_print_sam_hdr(const bntseq_t *bns, const char *rg_line);
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#ifdef USE_HTSLIB
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void bwa_format_sam_hdr(const bntseq_t *bns, const char *rg_line, kstring_t *str);
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#endif
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char *bwa_set_rg(const char *s);
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#ifdef USE_HTSLIB
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bams_t *bams_init();
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void bams_add(bams_t *bams, bam1_t *b);
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void bams_destroy(bams_t *bams);
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#endif
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#ifdef __cplusplus
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}
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#endif
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42
bwamem.c
42
bwamem.c
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@ -15,6 +15,10 @@
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#include "ksort.h"
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#include "utils.h"
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#ifdef USE_HTSLIB
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#include <htslib/sam.h>
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#endif
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#ifdef USE_MALLOC_WRAPPERS
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# include "malloc_wrap.h"
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#endif
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@ -805,7 +809,7 @@ static inline int get_rlen(int n_cigar, const uint32_t *cigar)
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return l;
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}
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void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m_, int softclip_all)
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void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m_, int softclip_all, bam_hdr_t *h)
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{
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int i, l_name;
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mem_aln_t ptmp = list[which], *p = &ptmp, mtmp, *m = 0; // make a copy of the alignment to convert
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@ -922,6 +926,15 @@ void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const m
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if (p->XA) { kputsn("\tXA:Z:", 6, str); kputs(p->XA, str); }
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if (s->comment) { kputc('\t', str); kputs(s->comment, str); }
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kputc('\n', str);
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#ifdef USE_HTSLIB
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bam1_t *b = bam_init1();
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if (sam_parse1(str, h, b) < 0) {
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// TODO: error!
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}
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bams_add(s->bams, b);
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str->l = 0; str->s = 0;
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#endif
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}
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/************************
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@ -955,7 +968,7 @@ int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
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}
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// TODO (future plan): group hits into a uint64_t[] array. This will be cleaner and more flexible
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void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m)
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void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m, bam_hdr_t *h)
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{
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extern char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, mem_alnreg_v *a, int l_query, const char *query);
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kstring_t str;
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@ -987,14 +1000,16 @@ void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pa
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mem_aln_t t;
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t = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, 0);
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t.flag |= extra_flag;
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mem_aln2sam(bns, &str, s, 1, &t, 0, m, opt->flag&MEM_F_SOFTCLIP);
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mem_aln2sam(bns, &str, s, 1, &t, 0, m, opt->flag&MEM_F_SOFTCLIP, h);
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} else {
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for (k = 0; k < aa.n; ++k)
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mem_aln2sam(bns, &str, s, aa.n, aa.a, k, m, opt->flag&MEM_F_SOFTCLIP);
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mem_aln2sam(bns, &str, s, aa.n, aa.a, k, m, opt->flag&MEM_F_SOFTCLIP, h);
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for (k = 0; k < aa.n; ++k) free(aa.a[k].cigar);
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free(aa.a);
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}
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#ifndef USE_HTSLIB
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s->sam = str.s;
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#endif
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if (XA) {
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for (k = 0; k < a->n; ++k) free(XA[k]);
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free(XA);
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@ -1120,6 +1135,7 @@ typedef struct {
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bseq1_t *seqs;
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mem_alnreg_v *regs;
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int64_t n_processed;
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bam_hdr_t *h;
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} worker_t;
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static void worker1(void *data, int i, int tid)
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@ -1138,26 +1154,33 @@ static void worker1(void *data, int i, int tid)
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static void worker2(void *data, int i, int tid)
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{
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extern int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], uint64_t id, bseq1_t s[2], mem_alnreg_v a[2]);
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extern int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], uint64_t id, bseq1_t s[2], mem_alnreg_v a[2], bam_hdr_t *h);
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extern void mem_reg2ovlp(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a);
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worker_t *w = (worker_t*)data;
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if (!(w->opt->flag&MEM_F_PE)) {
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#ifdef USE_HTSLIB
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w->seqs[i].bams = bams_init();
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#endif
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if (bwa_verbose >= 4) printf("=====> Finalizing read '%s' <=====\n", w->seqs[i].name);
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if (w->opt->flag & MEM_F_ALN_REG) {
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mem_reg2ovlp(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i]);
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} else {
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mem_mark_primary_se(w->opt, w->regs[i].n, w->regs[i].a, w->n_processed + i);
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mem_reg2sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0);
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mem_reg2sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0, w->h);
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}
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free(w->regs[i].a);
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} else {
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if (bwa_verbose >= 4) printf("=====> Finalizing read pair '%s' <=====\n", w->seqs[i<<1|0].name);
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mem_sam_pe(w->opt, w->bns, w->pac, w->pes, (w->n_processed>>1) + i, &w->seqs[i<<1], &w->regs[i<<1]);
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#ifdef USE_HTSLIB
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w->seqs[i<<1].bams = bams_init();
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w->seqs[1+(i<<1)].bams = bams_init();
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#endif
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mem_sam_pe(w->opt, w->bns, w->pac, w->pes, (w->n_processed>>1) + i, &w->seqs[i<<1], &w->regs[i<<1], w->h);
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free(w->regs[i<<1|0].a); free(w->regs[i<<1|1].a);
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}
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}
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void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int64_t n_processed, int n, bseq1_t *seqs, const mem_pestat_t *pes0)
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void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int64_t n_processed, int n, bseq1_t *seqs, const mem_pestat_t *pes0, bam_hdr_t *h)
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{
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extern void kt_for(int n_threads, void (*func)(void*,int,int), void *data, int n);
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worker_t w;
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@ -1169,12 +1192,13 @@ void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bn
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ctime = cputime(); rtime = realtime();
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global_bns = bns;
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regs = malloc(n * sizeof(mem_alnreg_v));
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w.opt = opt; w.bwt = bwt; w.bns = bns; w.pac = pac;
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w.opt = opt; w.bwt = bwt; w.bns = bns; w.pac = pac;
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w.seqs = seqs; w.regs = regs; w.n_processed = n_processed;
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w.pes = &pes[0];
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w.aux = malloc(opt->n_threads * sizeof(smem_aux_t));
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for (i = 0; i < opt->n_threads; ++i)
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w.aux[i] = smem_aux_init();
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w.h = h;
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kt_for(opt->n_threads, worker1, &w, (opt->flag&MEM_F_PE)? n>>1 : n); // find mapping positions
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for (i = 0; i < opt->n_threads; ++i)
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smem_aux_destroy(w.aux[i]);
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6
bwamem.h
6
bwamem.h
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@ -50,6 +50,9 @@ typedef struct {
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int max_matesw; // perform maximally max_matesw rounds of mate-SW for each end
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int max_hits; // if there are max_hits or fewer, output them all
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int8_t mat[25]; // scoring matrix; mat[0] == 0 if unset
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#ifdef USE_HTSLIB
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int bam_output;
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#endif
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} mem_opt_t;
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typedef struct {
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@ -123,8 +126,9 @@ extern "C" {
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* @param seqs query sequences; $seqs[i].seq/sam to be modified after the call
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* @param pes0 insert-size info; if NULL, infer from data; if not NULL, it should be an array with 4 elements,
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* corresponding to each FF, FR, RF and RR orientation. See mem_pestat() for more info.
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* @param h the BAM header, NULL if not using HTSLIB
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*/
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void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int64_t n_processed, int n, bseq1_t *seqs, const mem_pestat_t *pes0);
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void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int64_t n_processed, int n, bseq1_t *seqs, const mem_pestat_t *pes0, bam_hdr_t *h);
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/**
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* Find the aligned regions for one query sequence
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@ -80,7 +80,11 @@ mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *
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return ar;
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}
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#ifdef USE_HTSLIB
|
||||
void mem_reg2ovlp(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, bam_hdr_t *h)
|
||||
#else
|
||||
void mem_reg2ovlp(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a)
|
||||
#endif
|
||||
{
|
||||
int i;
|
||||
kstring_t str = {0,0,0};
|
||||
|
|
@ -102,7 +106,15 @@ void mem_reg2ovlp(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
|
|||
ksprintf(&str, "%.3f", (double)p->truesc / opt->a / (qe - qb > re - rb? qe - qb : re - rb));
|
||||
kputc('\n', &str);
|
||||
}
|
||||
#ifdef USE_HTSLIB
|
||||
bam1_t *b = bam_init1();
|
||||
if (sam_parse1(&str, h, b) < 0) {
|
||||
// TODO: error!
|
||||
}
|
||||
bams_add(s->bams, b);
|
||||
#else
|
||||
s->sam = str.s;
|
||||
#endif
|
||||
}
|
||||
|
||||
// Okay, returning strings is bad, but this has happened a lot elsewhere. If I have time, I need serious code cleanup.
|
||||
|
|
|
|||
|
|
@ -242,12 +242,12 @@ int mem_pair(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, cons
|
|||
|
||||
#define raw_mapq(diff, a) ((int)(6.02 * (diff) / (a) + .499))
|
||||
|
||||
int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], uint64_t id, bseq1_t s[2], mem_alnreg_v a[2])
|
||||
int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], uint64_t id, bseq1_t s[2], mem_alnreg_v a[2], bam_hdr_t *header)
|
||||
{
|
||||
extern void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a, int64_t id);
|
||||
extern int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a);
|
||||
extern void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m);
|
||||
extern void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m, int softclip_all);
|
||||
extern void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m, bam_hdr_t *h);
|
||||
extern void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m, int softclip_all, bam_hdr_t *h);
|
||||
extern char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_alnreg_v *a, int l_query, const char *query);
|
||||
|
||||
int n = 0, i, j, z[2], o, subo, n_sub, extra_flag = 1;
|
||||
|
|
@ -327,8 +327,14 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
|
|||
// write SAM
|
||||
h[0] = mem_reg2aln(opt, bns, pac, s[0].l_seq, s[0].seq, &a[0].a[z[0]]); h[0].mapq = q_se[0]; h[0].flag |= 0x40 | extra_flag; h[0].XA = XA[0]? XA[0][z[0]] : 0;
|
||||
h[1] = mem_reg2aln(opt, bns, pac, s[1].l_seq, s[1].seq, &a[1].a[z[1]]); h[1].mapq = q_se[1]; h[1].flag |= 0x80 | extra_flag; h[1].XA = XA[1]? XA[1][z[1]] : 0;
|
||||
mem_aln2sam(bns, &str, &s[0], 1, &h[0], 0, &h[1], opt->flag&MEM_F_SOFTCLIP); s[0].sam = strdup(str.s); str.l = 0;
|
||||
mem_aln2sam(bns, &str, &s[1], 1, &h[1], 0, &h[0], opt->flag&MEM_F_SOFTCLIP); s[1].sam = str.s;
|
||||
mem_aln2sam(bns, &str, &s[0], 1, &h[0], 0, &h[1], opt->flag&MEM_F_SOFTCLIP, header);
|
||||
#ifndef USE_HTSLIB
|
||||
s[0].sam = strdup(str.s); str.l = 0; /// not using HTSLIB
|
||||
#endif
|
||||
mem_aln2sam(bns, &str, &s[1], 1, &h[1], 0, &h[0], opt->flag&MEM_F_SOFTCLIP, header);
|
||||
#ifndef USE_HTSLIB
|
||||
s[1].sam = str.s; // not using HTSLIB
|
||||
#endif
|
||||
if (strcmp(s[0].name, s[1].name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", s[0].name, s[1].name);
|
||||
free(h[0].cigar); // h[0].XA will be freed in the following block
|
||||
free(h[1].cigar);
|
||||
|
|
@ -354,8 +360,8 @@ no_pairing:
|
|||
d = mem_infer_dir(bns->l_pac, a[0].a[0].rb, a[1].a[0].rb, &dist);
|
||||
if (!pes[d].failed && dist >= pes[d].low && dist <= pes[d].high) extra_flag |= 2;
|
||||
}
|
||||
mem_reg2sam_se(opt, bns, pac, &s[0], &a[0], 0x41|extra_flag, &h[1]);
|
||||
mem_reg2sam_se(opt, bns, pac, &s[1], &a[1], 0x81|extra_flag, &h[0]);
|
||||
mem_reg2sam_se(opt, bns, pac, &s[0], &a[0], 0x41|extra_flag, &h[1], header);
|
||||
mem_reg2sam_se(opt, bns, pac, &s[1], &a[1], 0x81|extra_flag, &h[0], header);
|
||||
if (strcmp(s[0].name, s[1].name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", s[0].name, s[1].name);
|
||||
free(h[0].cigar); free(h[1].cigar);
|
||||
return n;
|
||||
|
|
|
|||
44
bwaseqio.c
44
bwaseqio.c
|
|
@ -2,7 +2,11 @@
|
|||
#include <ctype.h>
|
||||
#include "bwtaln.h"
|
||||
#include "utils.h"
|
||||
#ifdef USE_HTSLIB
|
||||
#include <htslib/sam.h>
|
||||
#else
|
||||
#include "bamlite.h"
|
||||
#endif
|
||||
|
||||
#include "kseq.h"
|
||||
KSEQ_DECLARE(gzFile)
|
||||
|
|
@ -17,7 +21,12 @@ static char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4
|
|||
struct __bwa_seqio_t {
|
||||
// for BAM input
|
||||
int is_bam, which; // 1st bit: read1, 2nd bit: read2, 3rd: SE
|
||||
#ifdef USE_HTSLIB
|
||||
samFile *fp;
|
||||
bam_hdr_t *h;
|
||||
#else
|
||||
bamFile fp;
|
||||
#endif
|
||||
// for fastq input
|
||||
kseq_t *ks;
|
||||
};
|
||||
|
|
@ -25,14 +34,24 @@ struct __bwa_seqio_t {
|
|||
bwa_seqio_t *bwa_bam_open(const char *fn, int which)
|
||||
{
|
||||
bwa_seqio_t *bs;
|
||||
#ifndef USE_HTSLIB
|
||||
bam_header_t *h;
|
||||
#endif
|
||||
bs = (bwa_seqio_t*)calloc(1, sizeof(bwa_seqio_t));
|
||||
bs->is_bam = 1;
|
||||
bs->which = which;
|
||||
#ifdef USE_HTSLIB
|
||||
bs->fp = sam_open(fn, "rb");
|
||||
#else
|
||||
bs->fp = bam_open(fn, "r");
|
||||
#endif
|
||||
if (0 == bs->fp) err_fatal_simple("Couldn't open bam file");
|
||||
#ifdef USE_HTSLIB
|
||||
bs->h = sam_hdr_read(bs->fp);
|
||||
#else
|
||||
h = bam_header_read(bs->fp);
|
||||
bam_header_destroy(h);
|
||||
#endif
|
||||
return bs;
|
||||
}
|
||||
|
||||
|
|
@ -50,7 +69,12 @@ void bwa_seq_close(bwa_seqio_t *bs)
|
|||
{
|
||||
if (bs == 0) return;
|
||||
if (bs->is_bam) {
|
||||
#ifdef USE_HTSLIB
|
||||
if (0 != sam_close(bs->fp)) err_fatal_simple("Error closing sam/bam file");
|
||||
bam_hdr_destroy(bs->h);
|
||||
#else
|
||||
if (0 != bam_close(bs->fp)) err_fatal_simple("Error closing bam file");
|
||||
#endif
|
||||
} else {
|
||||
err_gzclose(bs->ks->f->f);
|
||||
kseq_destroy(bs->ks);
|
||||
|
|
@ -101,7 +125,11 @@ static bwa_seq_t *bwa_read_bam(bwa_seqio_t *bs, int n_needed, int *n, int is_com
|
|||
b = bam_init1();
|
||||
n_seqs = 0;
|
||||
seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
|
||||
#ifdef USE_HTSLIB
|
||||
while ((res = sam_read1(bs->fp, bs->h, b)) >= 0) {
|
||||
#else
|
||||
while ((res = bam_read1(bs->fp, b)) >= 0) {
|
||||
#endif
|
||||
uint8_t *s, *q;
|
||||
int go = 0;
|
||||
if ((bs->which & 1) && (b->core.flag & BAM_FREAD1)) go = 1;
|
||||
|
|
@ -114,14 +142,26 @@ static bwa_seq_t *bwa_read_bam(bwa_seqio_t *bs, int n_needed, int *n, int is_com
|
|||
p->qual = 0;
|
||||
p->full_len = p->clip_len = p->len = l;
|
||||
n_tot += p->full_len;
|
||||
#ifdef USE_HTSLIB
|
||||
s = bam_get_seq(b); q = bam_get_qual(b);
|
||||
#else
|
||||
s = bam1_seq(b); q = bam1_qual(b);
|
||||
#endif
|
||||
p->seq = (ubyte_t*)calloc(p->len + 1, 1);
|
||||
p->qual = (ubyte_t*)calloc(p->len + 1, 1);
|
||||
for (i = 0; i != p->full_len; ++i) {
|
||||
#ifdef USE_HTSLIB
|
||||
p->seq[i] = bam_nt16_nt4_table[(int)bam_seqi(s, i)];
|
||||
#else
|
||||
p->seq[i] = bam_nt16_nt4_table[(int)bam1_seqi(s, i)];
|
||||
#endif
|
||||
p->qual[i] = q[i] + 33 < 126? q[i] + 33 : 126;
|
||||
}
|
||||
#ifdef USE_HTSLIB
|
||||
if (bam_is_rev(b)) { // then reverse
|
||||
#else
|
||||
if (bam1_strand(b)) { // then reverse
|
||||
#endif
|
||||
seq_reverse(p->len, p->seq, 1);
|
||||
seq_reverse(p->len, p->qual, 0);
|
||||
}
|
||||
|
|
@ -130,7 +170,11 @@ static bwa_seq_t *bwa_read_bam(bwa_seqio_t *bs, int n_needed, int *n, int is_com
|
|||
memcpy(p->rseq, p->seq, p->len);
|
||||
seq_reverse(p->len, p->seq, 0); // *IMPORTANT*: will be reversed back in bwa_refine_gapped()
|
||||
seq_reverse(p->len, p->rseq, is_comp);
|
||||
#ifdef USE_HTSLIB
|
||||
p->name = strdup((const char*)bam_get_qname(b));
|
||||
#else
|
||||
p->name = strdup((const char*)bam1_qname(b));
|
||||
#endif
|
||||
if (n_seqs == n_needed) break;
|
||||
}
|
||||
if (res < 0 && res != -1) err_fatal_simple("Error reading bam file");
|
||||
|
|
|
|||
59
fastmap.c
59
fastmap.c
|
|
@ -53,7 +53,11 @@ int main_mem(int argc, char *argv[])
|
|||
|
||||
opt = mem_opt_init();
|
||||
memset(&opt0, 0, sizeof(mem_opt_t));
|
||||
#ifdef USE_HTSLIB
|
||||
while ((c = getopt(argc, argv, "epaFMCSPHYk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:o:")) >= 0) {
|
||||
#else
|
||||
while ((c = getopt(argc, argv, "epaFMCSPHYk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:")) >= 0) {
|
||||
#endif
|
||||
if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
|
||||
else if (c == 'x') mode = optarg;
|
||||
else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
|
||||
|
|
@ -120,7 +124,13 @@ int main_mem(int argc, char *argv[])
|
|||
if (bwa_verbose >= 3)
|
||||
fprintf(stderr, "[M::%s] mean insert size: %.3f, stddev: %.3f, max: %d, min: %d\n",
|
||||
__func__, pes[1].avg, pes[1].std, pes[1].high, pes[1].low);
|
||||
#ifdef USE_HTSLIB
|
||||
} else if (c == 'o') {
|
||||
opt->bam_output = atoi(optarg);
|
||||
}
|
||||
#else
|
||||
}
|
||||
#endif
|
||||
else return 1;
|
||||
}
|
||||
if (opt->n_threads < 1) opt->n_threads = 1;
|
||||
|
|
@ -165,6 +175,9 @@ int main_mem(int argc, char *argv[])
|
|||
fprintf(stderr, " specify the mean, standard deviation (10%% of the mean if absent), max\n");
|
||||
fprintf(stderr, " (4 sigma from the mean if absent) and min of the insert size distribution.\n");
|
||||
fprintf(stderr, " FR orientation only. [inferred]\n");
|
||||
#ifdef USE_HTSLIB
|
||||
fprintf(stderr, " -o INT 0 - BAM (compressed), 1 - BAM (uncompressed), 2 - SAM [%d]\n", opt->bam_output);
|
||||
#endif
|
||||
fprintf(stderr, "\n");
|
||||
fprintf(stderr, "Note: Please read the man page for detailed description of the command line and options.\n");
|
||||
fprintf(stderr, "\n");
|
||||
|
|
@ -226,8 +239,33 @@ int main_mem(int argc, char *argv[])
|
|||
opt->flag |= MEM_F_PE;
|
||||
}
|
||||
}
|
||||
if (!(opt->flag & MEM_F_ALN_REG))
|
||||
bam_hdr_t *h = NULL; // TODO
|
||||
#ifdef USE_HTSLIB
|
||||
samFile *out = NULL;
|
||||
char *modes[] = {"wb", "wbu", "w"};
|
||||
switch (opt->bam_output) {
|
||||
case 0: // BAM compressed
|
||||
case 1: // BAM uncompressed
|
||||
case 2: // SAM
|
||||
out = sam_open("-", modes[opt->bam_output]);
|
||||
break;
|
||||
default:
|
||||
fprintf(stderr, "Error: output format was out of range [%d]\n", opt->bam_output);
|
||||
return 1;
|
||||
}
|
||||
#endif
|
||||
if (!(opt->flag & MEM_F_ALN_REG)) {
|
||||
#ifdef USE_HTSLIB
|
||||
kstring_t str;
|
||||
str.l = str.m = 0; str.s = 0;
|
||||
bwa_format_sam_hdr(idx->bns, rg_line, &str);
|
||||
h = sam_hdr_parse(str.l, str.s);
|
||||
h->l_text = str.l; h->text = str.s;
|
||||
sam_hdr_write(out, h);
|
||||
#else
|
||||
bwa_print_sam_hdr(idx->bns, rg_line);
|
||||
#endif
|
||||
}
|
||||
while ((seqs = bseq_read(opt->chunk_size * opt->n_threads, &n, ks, ks2)) != 0) {
|
||||
int64_t size = 0;
|
||||
if ((opt->flag & MEM_F_PE) && (n&1) == 1) {
|
||||
|
|
@ -242,11 +280,22 @@ int main_mem(int argc, char *argv[])
|
|||
for (i = 0; i < n; ++i) size += seqs[i].l_seq;
|
||||
if (bwa_verbose >= 3)
|
||||
fprintf(stderr, "[M::%s] read %d sequences (%ld bp)...\n", __func__, n, (long)size);
|
||||
mem_process_seqs(opt, idx->bwt, idx->bns, idx->pac, n_processed, n, seqs, pes0);
|
||||
mem_process_seqs(opt, idx->bwt, idx->bns, idx->pac, n_processed, n, seqs, pes0, h);
|
||||
n_processed += n;
|
||||
for (i = 0; i < n; ++i) {
|
||||
#ifdef USE_HTSLIB
|
||||
if (seqs[i].bams) {
|
||||
int j;
|
||||
for (j = 0; j < seqs[i].bams->l; j++) {
|
||||
sam_write1(out, h, seqs[i].bams->bams[j]);
|
||||
}
|
||||
}
|
||||
bams_destroy(seqs[i].bams); seqs[i].bams = NULL;
|
||||
#else
|
||||
if (seqs[i].sam) err_fputs(seqs[i].sam, stdout);
|
||||
free(seqs[i].name); free(seqs[i].comment); free(seqs[i].seq); free(seqs[i].qual); free(seqs[i].sam);
|
||||
free(seqs[i].sam);
|
||||
#endif
|
||||
free(seqs[i].name); free(seqs[i].comment); free(seqs[i].seq); free(seqs[i].qual);
|
||||
}
|
||||
free(seqs);
|
||||
}
|
||||
|
|
@ -255,6 +304,10 @@ int main_mem(int argc, char *argv[])
|
|||
bwa_idx_destroy(idx);
|
||||
kseq_destroy(ks);
|
||||
err_gzclose(fp); kclose(ko);
|
||||
#ifdef USE_HTSLIB
|
||||
sam_close(out);
|
||||
bam_hdr_destroy(h);
|
||||
#endif
|
||||
if (ks2) {
|
||||
kseq_destroy(ks2);
|
||||
err_gzclose(fp2); kclose(ko2);
|
||||
|
|
|
|||
7
main.c
7
main.c
|
|
@ -86,8 +86,15 @@ int main(int argc, char *argv[])
|
|||
fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
|
||||
return 1;
|
||||
}
|
||||
#ifdef USE_HTSLIB
|
||||
if (strcmp(argv[1], "mem") != 0) {
|
||||
err_fflush(stdout);
|
||||
err_fclose(stdout);
|
||||
}
|
||||
#else
|
||||
err_fflush(stdout);
|
||||
err_fclose(stdout);
|
||||
#endif
|
||||
if (ret == 0) {
|
||||
fprintf(stderr, "[%s] Version: %s\n", __func__, PACKAGE_VERSION);
|
||||
fprintf(stderr, "[%s] CMD:", __func__);
|
||||
|
|
|
|||
Loading…
Reference in New Issue