bwa基因比对程序

bwa算法，经过bwa算法执行后会得到sam文件，sam文件用于之后的gatk工作

#include 
#include 
#include 
#include 
#include 
#include “bamlite.h“

#ifdef USE_MALLOC_WRAPPERS
#  include “malloc_wrap.h“
#endif

/*********************
 * from bam_endian.c *
 *********************/

static inline int bam_is_big_endian（）
{
	long one= 1;
	return !（*（（char *）（&one）））;
}
static inline uint16_t bam_swap_endian_2（uint16_t v）
{
	return （uint16_t）（（（v & 0x00FF00FFU） << 8） | （（v & 0xFF00FF00U） >> 8））;
}
static inline void *bam_swap_endian_2p（void *x）
{
	*（uint16_t*）x = bam_swap_endian_2（*（uint16_t*）x）;
	return x;
}
static inline uint32_t bam_swap_endian_4（uint32_t v）
{
	v = （（v & 0x0000FFFFU） << 16） | （v >> 16）;
	return （（v & 0x00FF00FFU） << 8） | （（v & 0xFF00FF00U） >> 8）;
}
static inline void *bam_swap_endian_4p（void *x）
{
	*（uint32_t*）x = bam_swap_endian_4（*（uint32_t*）x）;
	return x;
}
static inline uint64_t bam_swap_endian_8（uint64_t v）
{
	v = （（v & 0x00000000FFFFFFFFLLU） << 32） | （v >> 32）;
	v = （（v & 0x0000FFFF0000FFFFLLU） << 16） | （（v & 0xFFFF0000FFFF0000LLU） >> 16）;
	return （（v & 0x00FF00FF00FF00FFLLU） << 8） | （（v & 0xFF00FF00FF00FF00LLU） >> 8）;
}
static inline void *bam_swap_endian_8p（void *x）
{
	*（uint64_t*）x = bam_swap_endian_8（*（uint64_t*）x）;
	return x;
}

/**************
 * from bam.c *
 **************/

int bam_is_be;

bam_header_t *bam_header_init（）
{
	bam_is_be = bam_is_big_endian（）;
	return （bam_header_t*）calloc（1 sizeof（bam_header_t））;
}

void bam_header_destroy（bam_header_t *header）
{
	int32_t i;
	if （header == 0） return;
	if （header->target_name） {
		for （i = 0; i < header->n_targets; ++i）
			if （header->target_name[i]） free（header->target_name[i]）;
		if （header->target_len） free（header->target_len）;
		free（header->target_name）;
	}
	if （header->text） free（header->text）;
	free（header）;
}

bam_header_t *bam_header_read（bamFile fp）
{
	bam_header_t *header;
	char buf[4];
	int magic_len;
	int32_t i = 1 name_len;
	// read “BAM1“
	magic_len = bam_read（fp buf 4）;
	if （magic_len != 4 || strncmp（buf “BAM\001“ 4） != 0） {
		fprintf（stderr “[bam_header_read] invalid BAM binary header （this is not a BAM file）.\n“）;
		return NULL;
	}
	header = bam_header_init（）;
	// read plain text and the number of reference sequences
	if （bam_read（fp &header->l_text 4） != 4） goto fail; 
	if （bam_is_be） bam_swap_endian_4p（&header->l_text）;
	header->text = （char*）calloc（header->l_text + 1 1）;
	if （bam_read（fp header->text header->l_text） != header->l_text） goto fail;
	if （bam_read（fp &header->n_targets 4） != 4） goto fail;
	if （bam_is_be） bam_swap_endian_4p（&header->n_targets）;
	// read reference sequence names and lengths
	header->target_name = （char**）calloc（header->n_targets sizeof（char*））;
	header->target_len = （uint32_t*）calloc（header->n_targets 4）;
	for （i = 0; i != header->n_targets; ++i） {
		if （bam_read（fp &name_len 4） != 4） goto fail;
		if （bam_is_be） bam_swap_endian_4p（&name_len）;
		header->target_name[i] = （char*）calloc（name_len 1）;
		if （bam_read（fp header->target_name[

 属性            大小     日期    时间   名称
----------- ---------  ---------- -----  ----

    .......        55  2016-05-31 23:02  bwa-master\bwa-master\.gitignore

    .......        53  2016-05-31 23:02  bwa-master\bwa-master\.travis.yml

    .......      6098  2016-05-31 23:02  bwa-master\bwa-master\bamlite.c

    .......      3124  2016-05-31 23:02  bwa-master\bwa-master\bamlite.h

    .......     13778  2016-05-31 23:02  bwa-master\bwa-master\bntseq.c

    .......      2775  2016-05-31 23:02  bwa-master\bwa-master\bntseq.h

    .......     26165  2016-05-31 23:02  bwa-master\bwa-master\bwa.1

    .......     13684  2016-05-31 23:02  bwa-master\bwa-master\bwa.c

    .......      2044  2016-05-31 23:02  bwa-master\bwa-master\bwa.h

    .......     17977  2016-05-31 23:02  bwa-master\bwa-master\bwakit\bwa-postalt.js

    .......      5953  2016-05-31 23:02  bwa-master\bwa-master\bwakit\README.md

    .......      6604  2016-05-31 23:02  bwa-master\bwa-master\bwakit\run-bwamem

    .......      1731  2016-05-31 23:02  bwa-master\bwa-master\bwakit\run-gen-ref

    .......       411  2016-05-31 23:02  bwa-master\bwa-master\bwakit\run-HLA

    .......      1681  2016-05-31 23:02  bwa-master\bwa-master\bwakit\typeHLA-selctg.js

    .......     16856  2016-05-31 23:02  bwa-master\bwa-master\bwakit\typeHLA.js

    .......      1521  2016-05-31 23:02  bwa-master\bwa-master\bwakit\typeHLA.sh

    .......     47544  2016-05-31 23:02  bwa-master\bwa-master\bwamem.c

    .......      7958  2016-05-31 23:02  bwa-master\bwa-master\bwamem.h

    .......      4428  2016-05-31 23:02  bwa-master\bwa-master\bwamem_extra.c

    .......     17361  2016-05-31 23:02  bwa-master\bwa-master\bwamem_pair.c

    .......     29383  2016-05-31 23:02  bwa-master\bwa-master\bwape.c

    .......     19552  2016-05-31 23:02  bwa-master\bwa-master\bwase.c

    .......      1033  2016-05-31 23:02  bwa-master\bwa-master\bwase.h

    .......      6868  2016-05-31 23:02  bwa-master\bwa-master\bwaseqio.c

    .......      5816  2016-05-31 23:02  bwa-master\bwa-master\bwashm.c

    .......     15342  2016-05-31 23:02  bwa-master\bwa-master\bwt.c

    .......      4966  2016-05-31 23:02  bwa-master\bwa-master\bwt.h

    .......     11004  2016-05-31 23:02  bwa-master\bwa-master\bwtaln.c

    .......      3833  2016-05-31 23:02  bwa-master\bwa-master\bwtaln.h

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