diff bwa-0.6.2/bamlite.h @ 2:a294fbfcb1db draft default tip

Uploaded BWA

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa-0.6.2/bamlite.h	Fri Jul 18 07:55:59 2014 -0400
@@ -0,0 +1,94 @@
+#ifndef BAMLITE_H_
+#define BAMLITE_H_
+
+#include <stdint.h>
+#include <zlib.h>
+
+typedef gzFile bamFile;
+#define bam_open(fn, mode) gzopen(fn, mode)
+#define bam_dopen(fd, mode) gzdopen(fd, mode)
+#define bam_close(fp) gzclose(fp)
+#define bam_read(fp, buf, size) gzread(fp, buf, size)
+
+typedef struct {
+	int32_t n_targets;
+	char **target_name;
+	uint32_t *target_len;
+	size_t l_text, n_text;
+	char *text;
+} bam_header_t;
+
+#define BAM_FPAIRED        1
+#define BAM_FPROPER_PAIR   2
+#define BAM_FUNMAP         4
+#define BAM_FMUNMAP        8
+#define BAM_FREVERSE      16
+#define BAM_FMREVERSE     32
+#define BAM_FREAD1        64
+#define BAM_FREAD2       128
+#define BAM_FSECONDARY   256
+#define BAM_FQCFAIL      512
+#define BAM_FDUP        1024
+
+#define BAM_CIGAR_SHIFT 4
+#define BAM_CIGAR_MASK  ((1 << BAM_CIGAR_SHIFT) - 1)
+
+#define BAM_CMATCH      0
+#define BAM_CINS        1
+#define BAM_CDEL        2
+#define BAM_CREF_SKIP   3
+#define BAM_CSOFT_CLIP  4
+#define BAM_CHARD_CLIP  5
+#define BAM_CPAD        6
+
+typedef struct {
+	int32_t tid;
+	int32_t pos;
+	uint32_t bin:16, qual:8, l_qname:8;
+	uint32_t flag:16, n_cigar:16;
+	int32_t l_qseq;
+	int32_t mtid;
+	int32_t mpos;
+	int32_t isize;
+} bam1_core_t;
+
+typedef struct {
+	bam1_core_t core;
+	int l_aux, data_len, m_data;
+	uint8_t *data;
+} bam1_t;
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
+#define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
+#define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))
+#define bam1_qname(b) ((char*)((b)->data))
+#define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname)
+#define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))
+#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
+#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)
+
+#define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
+#define bam_destroy1(b) do {					\
+		if (b) { free((b)->data); free(b); }	\
+	} while (0)
+
+extern int bam_is_be;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	bam_header_t *bam_header_init(void);
+	void bam_header_destroy(bam_header_t *header);
+	bam_header_t *bam_header_read(bamFile fp);
+	int bam_read1(bamFile fp, bam1_t *b);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif