#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））;
}
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）;
	return?（（v?&?0x00FF00FFU）?<>?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?=?（（v?&?0x0000FFFF0000FFFFLLU）?<>?16）;
	return?（（v?&?0x00FF00FF00FF00FFLLU）?<>?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?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[

?屬性????????????大小?????日期????時間???名稱
-----------?---------??----------?-----??----

????.......????????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

............此處省略53個文件信息