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/* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Primarily, this exists to drive our BAM/SAM parsing code
*/
#include <kapp/args.h>
#include <kapp/main.h>
#include <klib/log.h>
#include <kfs/file.h>
#include <stdlib.h>
#include <stdio.h>
#include "bam.h"
#include <klib/rc.h>
static void writeHeader(BAM_File const *const bam)
{
char const *header = NULL;
size_t hsize = 0;
BAM_FileGetHeaderText(bam, &header, &hsize);
fwrite(header, 1, hsize, stdout);
}
static char *buffer;
static size_t buffer_size;
static rc_t writeSAM(BAM_Alignment const *const rec)
{
if (buffer_size == 0) {
buffer_size = 64 * 1024;
buffer = malloc(buffer_size);
if (buffer == NULL)
return RC(rcAlign, rcRow, rcWriting, rcMemory, rcExhausted);
}
for ( ; ; ) {
size_t actsize = 0;
rc_t const rc = BAM_AlignmentFormatSAM(rec, &actsize, buffer_size, buffer);
if (rc == 0) {
fwrite(buffer, 1, actsize, stdout);
return 0;
}
if (GetRCObject(rc) == (int)rcData && GetRCState(rc) == (int)rcExcessive) {
void *tmp = realloc(buffer, buffer_size * 2);
if (tmp == NULL)
return RC(rcAlign, rcRow, rcWriting, rcMemory, rcExhausted);
buffer_size *= 2;
buffer = tmp;
}
else
return rc;
}
}
static
void samview(char const path[])
{
BAM_File const *bam = NULL;
rc_t rc = BAM_FileMake(&bam, NULL, NULL, path);
if (rc == 0) {
BAM_Alignment const *rec = NULL;
writeHeader(bam);
while ((rc = BAM_FileRead3(bam, &rec)) == 0) {
rc_t const rc2 = writeSAM(rec);
BAM_AlignmentRelease(rec);
if (rc2)
break;
}
BAM_FileRelease(bam);
if (GetRCObject(rc) == rcRow && GetRCState(rc) == rcNotFound)
rc = 0;
}
if (rc)
LOGERR(klogWarn, rc, "Final RC");
}
rc_t CC UsageSummary(char const *name)
{
return 0;
}
rc_t CC Usage(Args const *args)
{
return 0;
}
rc_t CC KMain(int argc, char *argv[])
{
if (argc == 1) {
samview("/dev/stdin");
return 0;
}
while (--argc) {
samview(*++argv);
}
return 0;
}
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