115 lines
3.1 KiB
C
115 lines
3.1 KiB
C
#ifndef BAMLITE_H_
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#define BAMLITE_H_
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#include <stdint.h>
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#include <zlib.h>
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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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#define USE_VERBOSE_ZLIB_WRAPPERS
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typedef gzFile bamFile;
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#ifdef USE_VERBOSE_ZLIB_WRAPPERS
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/* These print error messages on failure */
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# define bam_open(fn, mode) bamlite_gzopen(fn, mode)
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# define bam_dopen(fd, mode) gzdopen(fd, mode)
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# define bam_close(fp) bamlite_gzclose(fp)
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# define bam_read(fp, buf, size) bamlite_gzread(fp, buf, size)
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#else
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# define bam_open(fn, mode) gzopen(fn, mode)
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# define bam_dopen(fd, mode) gzdopen(fd, mode)
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# define bam_close(fp) gzclose(fp)
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# define bam_read(fp, buf, size) gzread(fp, buf, size)
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#endif /* USE_VERBOSE_ZLIB_WRAPPERS */
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typedef struct {
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int32_t n_targets;
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char **target_name;
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uint32_t *target_len;
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size_t l_text, n_text;
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char *text;
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} bam_header_t;
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#define BAM_FPAIRED 1
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#define BAM_FPROPER_PAIR 2
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#define BAM_FUNMAP 4
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#define BAM_FMUNMAP 8
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#define BAM_FREVERSE 16
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#define BAM_FMREVERSE 32
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#define BAM_FREAD1 64
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#define BAM_FREAD2 128
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#define BAM_FSECONDARY 256
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#define BAM_FQCFAIL 512
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#define BAM_FDUP 1024
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#define BAM_CIGAR_SHIFT 4
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#define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1)
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#define BAM_CMATCH 0
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#define BAM_CINS 1
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#define BAM_CDEL 2
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#define BAM_CREF_SKIP 3
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#define BAM_CSOFT_CLIP 4
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#define BAM_CHARD_CLIP 5
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#define BAM_CPAD 6
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typedef struct {
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int32_t tid;
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int32_t pos;
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uint32_t bin:16, qual:8, l_qname:8;
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uint32_t flag:16, n_cigar:16;
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int32_t l_qseq;
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int32_t mtid;
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int32_t mpos;
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int32_t isize;
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} bam1_core_t;
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typedef struct {
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bam1_core_t core;
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int l_aux, data_len, m_data;
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uint8_t *data;
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} bam1_t;
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#ifndef kroundup32
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#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
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#endif
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#define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
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#define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
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#define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))
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#define bam1_qname(b) ((char*)((b)->data))
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#define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname)
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#define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))
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#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
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#define bam1_aux(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (b)->core.l_qseq + ((b)->core.l_qseq + 1)/2)
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#define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
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#define bam_destroy1(b) do { \
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if (b) { free((b)->data); free(b); } \
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} while (0)
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extern int bam_is_be;
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#ifdef __cplusplus
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extern "C" {
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#endif
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bam_header_t *bam_header_init(void);
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void bam_header_destroy(bam_header_t *header);
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bam_header_t *bam_header_read(bamFile fp);
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int bam_read1(bamFile fp, bam1_t *b);
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#ifdef USE_VERBOSE_ZLIB_WRAPPERS
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gzFile bamlite_gzopen(const char *fn, const char *mode);
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int bamlite_gzread(gzFile file, void *ptr, unsigned int len);
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int bamlite_gzclose(gzFile file);
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#endif /* USE_VERBOSE_ZLIB_WRAPPERS */
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#ifdef __cplusplus
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}
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#endif
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#endif
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