static
rc_t CC AlignAccessAlignmentEnumeratorWhack(AlignAccessAlignmentEnumerator *self) {
if (self->innerSelf)
BAMAlignmentRelease(self->innerSelf);
AlignAccessDBRelease(self->parent);
return 0;
}
LIB_EXPORT rc_t CC AlignAccessMgrMakeIndexBAMDB(const AlignAccessMgr *self, const AlignAccessDB **db, const VPath *bam, const VPath *bam_index) {
rc_t rc = AlignAccessMgrMakeBAMDB(self, db, bam);
if (rc == 0) {
rc = BAMFileOpenIndexWithVPath((**db).innerSelf, bam_index);
if (rc == 0)
return 0;
AlignAccessDBRelease(*db);
*db = NULL;
}
return rc;
}
static
rc_t CC AlignAccessRefSeqEnumeratorWhack(AlignAccessRefSeqEnumerator *self) {
return AlignAccessDBRelease(self->parent);
}
int LowLevelTest()
{
cout << "Running LowLevelTest()." << endl;
const AlignAccessMgr* mgr = 0;
CALL(AlignAccessMgrMake(&mgr));
VFSManager* vfs_mgr;
CALL(VFSManagerMake(&vfs_mgr));
VPath* bam_path = 0;
#ifdef _MSC_VER
# define BAM_FILE "//traces04/1kg_pilot_data/ftp/pilot_data/data/NA10851/alignment/NA10851.SLX.maq.SRP000031.2009_08.bam"
#else
# define BAM_FILE "/netmnt/traces04/1kg_pilot_data/ftp/pilot_data/data/NA10851/alignment/NA10851.SLX.maq.SRP000031.2009_08.bam"
#endif
cout << "Testing BAM file: "<<BAM_FILE<<endl;
CALL(VFSManagerMakeSysPath(vfs_mgr, &bam_path, BAM_FILE));
VPath* bai_path = 0;
CALL(VFSManagerMakeSysPath(vfs_mgr, &bai_path, BAM_FILE ".bai"));
const AlignAccessDB* bam = 0;
CALL(AlignAccessMgrMakeIndexBAMDB(mgr, &bam, bam_path, bai_path));
#ifdef _MSC_VER
InitializeCriticalSection(&sdk_mutex);
#endif
const size_t kNumCursors = 8;
const size_t kNumThreads = 3;
SThreadInfo tinfo[kNumCursors];
const char* ids[kNumCursors] = {
"NT_113960",
"NT_113945",
"NT_113880",
"NT_113960",
"NT_113960",
"NT_113960",
"NT_113945",
"NT_113880"
};
for ( size_t i = 0; i < kNumThreads; ++i ) {
tinfo[i].init(i, bam, ids[i]);
}
for ( size_t i = 0; i < kNumThreads; ++i ) {
cout << "Starting thread " << i << " for " << ids[i] << endl;
#ifdef _MSC_VER
tinfo[i].thread_id = CreateThread(NULL, 0, read_thread_func,
&tinfo[i], 0, NULL);
#else
pthread_create(&tinfo[i].thread_id, 0, read_thread_func, &tinfo[i]);
#endif
}
for ( size_t i = 0; i < kNumThreads; ++i ) {
cout << "Waiting for thread " << i << endl;
void* ret = 0;
#ifdef _MSC_VER
WaitForSingleObject(tinfo[i].thread_id, INFINITE);
CloseHandle(tinfo[i].thread_id);
#else
pthread_join(tinfo[i].thread_id, &ret);
#endif
cout << "Align count: " << tinfo[i].count << endl;
}
CALL(AlignAccessDBRelease(bam));
CALL(VPathRelease(bam_path));
CALL(VPathRelease(bai_path));
CALL(AlignAccessMgrRelease(mgr));
CALL(VFSManagerRelease(vfs_mgr));
cout << "Success." << endl;
return 0;
}
