// File: /workspace/github_cpp_makefile_star2_O3/statgen[P]statgen/lib/samtools-0.1.7a-hybrid/bam.c
// Function: bam_header_read
bam_header_t *bam_header_read(bamFile fp)
{
	bam_header_t *header;
	char buf[4];
	int32_t i = 1, name_len;
	// check EOF
	i = bgzf_check_EOF(fp);
	if (i < 0) {
		// If the file is a pipe, checking the EOF marker will *always* fail
		// with ESPIPE.  Suppress the error message in this case.
		if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
	}
	else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent.\n");
	// read "BAM1"
	if (bam_read(fp, buf, 4) != 4) return 0;
	if (strncmp(buf, "BAM\001", 4)) {
		fprintf(stderr, "[bam_header_read] wrong header\n");
		return 0;
	}
	header = bam_header_init();
	// read plain text and the number of reference sequences
	bam_read(fp, &header->l_text, 4);
	if (bam_is_be) bam_swap_endian_4p(&header->l_text);
	header->text = (char*)calloc(header->l_text + 1, 1);
	bam_read(fp, header->text, header->l_text);
	bam_read(fp, &header->n_targets, 4);
	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) {
		bam_read(fp, &name_len, 4);
		if (bam_is_be) bam_swap_endian_4p(&name_len);
		header->target_name[i] = (char*)calloc(name_len, 1);
		bam_read(fp, header->target_name[i], name_len);
		bam_read(fp, &header->target_len[i], 4);
		if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
	}
	return header;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
callq 0x10e66
testl %eax, %eax
js 0x123a3
jne 0x123b1
callq 0x3e06
jmp 0x123b1
callq 0x34a0
cmpl $0x1d, (%rax)
jne 0x1254c
leaq 0x4(%rsp), %rsi
movq %rbx, %rdi
movl $0x4, %edx
callq 0x1096a
cmpl $0x4, %eax
jne 0x12537
cmpl $0x14d4142, 0x4(%rsp)   # imm = 0x14D4142
jne 0x12532
movl $0x0, 0x1cf3c(%rip)     # 0x2f320
movl $0x1, %edi
movl $0x40, %esi
callq 0x3530
movq %rax, %r14
movq %rax, %r12
addq $0x30, %r12
movq %rbx, %rdi
movq %r12, %rsi
movl $0x4, %edx
callq 0x1096a
cmpl $0x0, 0x1cf0c(%rip)     # 0x2f320
je 0x12423
movl (%r12), %r15d
bswapl %r15d
movl %r15d, (%r12)
jmp 0x12427
movl (%r12), %r15d
leal 0x1(%r15), %eax
movslq %eax, %rdi
movl $0x1, %esi
callq 0x3530
movq %rax, 0x38(%r14)
movq %rbx, %rdi
movq %rax, %rsi
movl %r15d, %edx
callq 0x1096a
movq %rbx, %rdi
movq %r14, %rsi
movl $0x4, %edx
callq 0x1096a
cmpl $0x0, 0x1cebf(%rip)     # 0x2f320
je 0x1246d
movl (%r14), %eax
bswapl %eax
movl %eax, (%r14)
jmp 0x12470
movl (%r14), %eax
movslq %eax, %r15
movl $0x8, %esi
movq %r15, %rdi
callq 0x3530
movq %rax, 0x8(%r14)
movl $0x4, %esi
movq %r15, %rdi
callq 0x3530
movq %rax, 0x10(%r14)
testl %r15d, %r15d
je 0x1253a
xorl %r13d, %r13d
movq %rsp, %r15
xorl %ebp, %ebp
movq %rbx, %rdi
movq %r15, %rsi
movl $0x4, %edx
callq 0x1096a
cmpl $0x0, 0x1ce63(%rip)     # 0x2f320
movl (%rsp), %eax
je 0x124c7
bswapl %eax
movl %eax, (%rsp)
movslq %eax, %r12
movl $0x1, %esi
movq %r12, %rdi
callq 0x3530
movq 0x8(%r14), %rcx
movq %rax, (%rcx,%r13,2)
movq 0x8(%r14), %rax
movq (%rax,%r13,2), %rsi
movq %rbx, %rdi
movl %r12d, %edx
callq 0x1096a
movq 0x10(%r14), %rsi
addq %r13, %rsi
movq %rbx, %rdi
movl $0x4, %edx
callq 0x1096a
cmpl $0x0, 0x1ce13(%rip)     # 0x2f320
je 0x1251d
movq 0x10(%r14), %rax
movl (%rax,%r13), %ecx
bswapl %ecx
movl %ecx, (%rax,%r13)
incq %rbp
movl (%r14), %eax
addq $0x4, %r13
cmpq %rax, %rbp
jne 0x124a6
jmp 0x1253a
callq 0x3e22
xorl %r14d, %r14d
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x12f2a(%rip), %rdi     # 0x2547d
callq 0x3620
jmp 0x123b1