int main()
{
samfile_t *in = 0, *out = 0;
int slx2sngr = 0;
char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
strcpy(in_mode, "r"); strcpy(out_mode, "w");
strcat(in_mode, "b");
printf("start******************************************************\n");
char *filename = "/ifs1/RD/shaohaojing/DAI/1000306/1000306_HUMgqbRLJDIAAPE_091015_I58_FC42UC6AAXX_L2_HUMgqbRLJDIAAPE_1.fq.bam.sort.bam";
if ((in = samopen(filename, in_mode, fn_list)) == 0)
{
fprintf(stderr, "[main_samview] fail to open file for reading.\n");
exit(0);
}
if (in->header == 0) {
fprintf(stderr, "[main_samview] fail to read the header.\n");
exit(0);
}
if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
fprintf(stderr, "[main_samview] fail to open file for writing.\n");
exit(0);
}
bam1_t *b = bam_init1();
int r;
char *s;
while((r = samread(in, b)) >= 0)
{
if (!__g_skip_aln(in->header, b)) {
s = bam_format1_core(out->header, b, out->type>>2&3);
}
printf("%s\n", s);
free(s);
// printf("%s", b->data);
// printf("\n++++++++++%d+++++++++++", r);
// printf("********************\n");
}
/**
* DATE: 2010-7-29
* FUNCTION: read a line from sam/bam file.
* PARAMETER: line: the read data will stored in this varible.
* RETURN: the line size when read successful. -1 when read failed
*/
int SamCtrl::readline(std::string &line)
{
if (m_in == 0)
{
return -1;
}
int ret = 0;
// begin to read
while ((ret = samread(m_in, m_b)) >= 0)
{
// when read failed continue
if (__g_skip_aln(m_in->header, m_b))
{
continue;
}
m_s = bam_format1_core(m_out->header, m_b, m_out->type>>2&3); // read the buffer
line = m_s; // store into the line
free(m_s);
return line.size();
}
return -1;
}
