void testBamIndex()
{
// BAM indexes are compressed, so can't be tested without zlib.
#ifdef __ZLIB_AVAILABLE__
// Create a bam index.
BamIndex bamIndex;
bamIndex.readIndex("testFiles/sortedBam.bam.bai");
testIndex(bamIndex);
BamIndexFileTest test1;
bool caughtException = false;
try
{
// Try reading the bam index without specifying a
// filename and before opening a bam file.
assert(test1.ReadBamIndex() == false);
}
catch (std::exception& e)
{
caughtException = true;
assert(strcmp(e.what(), "FAIL_ORDER: Failed to read the bam Index file - the BAM file needs to be read first in order to determine the index filename.") == 0);
}
// Should have failed and thrown an exception.
assert(caughtException);
// Read the bam index with a specified name.
assert(test1.ReadBamIndex("testFiles/sortedBam.bam.bai"));
BamIndex* index = test1.getBamIndex();
assert(index != NULL);
testIndex(*index);
// Open the bam file so the index can be opened.
assert(test1.OpenForRead("testFiles/sortedBam.bam"));
// Try reading the bam index without specifying a
// filename after opening a bam file.
assert(test1.ReadBamIndex() == true);
index = test1.getBamIndex();
assert(index != NULL);
testIndex(*index);
// Open the bam file so the index can be opened.
// This time the index file does not have .bam in it.
assert(test1.OpenForRead("testFiles/sortedBam2.bam"));
// Try reading the bam index without specifying a
// filename after opening a bam file.
assert(test1.ReadBamIndex() == true);
index = test1.getBamIndex();
assert(index != NULL);
testIndex(*index);
#endif
}
int
Runner::runCommandLine( int argc, const char *argv[] ) const
{
typedef std::deque<std::string> TestNames;
Runner subrunner;
for ( int index = 1; index < argc; ++index )
{
std::string opt = argv[index];
if ( opt == "--list-tests" )
{
listTests();
return 0;
}
else if ( opt == "--test-auto" )
{
preventDialogOnCrash();
}
else if ( opt == "--test" )
{
++index;
if ( index < argc )
{
unsigned int testNameIndex;
if ( testIndex( argv[index], testNameIndex ) )
{
subrunner.add( tests_[testNameIndex] );
}
else
{
fprintf( stderr, "Test '%s' does not exist!\n", argv[index] );
return 2;
}
}
else
{
printUsage( argv[0] );
return 2;
}
}
else
{
printUsage( argv[0] );
return 2;
}
}
bool succeeded;
if ( subrunner.testCount() > 0 )
{
succeeded = subrunner.runAllTest( subrunner.testCount() > 1 );
}
else
{
succeeded = runAllTest( true );
}
return succeeded ? 0
: 1;
}
int
main(int argc, char **argv) {
char *ovlName = NULL;
uint32 maxJob = 0;
bool deleteIntermediates = true;
bool doExplicitTest = false;
bool doFixes = false;
char name[FILENAME_MAX];
argc = AS_configure(argc, argv);
int err=0;
int arg=1;
while (arg < argc) {
if (strcmp(argv[arg], "-O") == 0) {
ovlName = argv[++arg];
} else if (strcmp(argv[arg], "-F") == 0) {
maxJob = atoi(argv[++arg]);
} else if (strcmp(argv[arg], "-f") == 0) {
doFixes = true;
} else if (strcmp(argv[arg], "-t") == 0) {
doExplicitTest = true;
ovlName = argv[++arg];
} else if (strcmp(argv[arg], "-nodelete") == 0) {
deleteIntermediates = false;
} else {
fprintf(stderr, "ERROR: unknown option '%s'\n", argv[arg]);
}
arg++;
}
if (ovlName == NULL)
err++;
if ((maxJob == 0) && (doExplicitTest == false))
err++;
if (err) {
fprintf(stderr, "usage: %s ...\n", argv[0]);
fprintf(stderr, " -O x.ovlStore path to overlap store to build the final index for\n");
fprintf(stderr, " -F s number of slices used in bucketizing/sorting\n");
fprintf(stderr, "\n");
fprintf(stderr, " -t x.ovlStore explicitly test a previously constructed index\n");
fprintf(stderr, " -f when testing, also create a new 'idx.fixed' which might\n");
fprintf(stderr, " resolve rare problems\n");
fprintf(stderr, "\n");
fprintf(stderr, " -nodelete do not remove intermediate files when the index is\n");
fprintf(stderr, " successfully created\n");
fprintf(stderr, "\n");
fprintf(stderr, " DANGER DO NOT USE DO NOT USE DO NOT USE DANGER\n");
fprintf(stderr, " DANGER DANGER\n");
fprintf(stderr, " DANGER This command is difficult to run by hand. DANGER\n");
fprintf(stderr, " DANGER Use ovStoreCreate instead. DANGER\n");
fprintf(stderr, " DANGER DANGER\n");
fprintf(stderr, " DANGER DO NOT USE DO NOT USE DO NOT USE DANGER\n");
fprintf(stderr, "\n");
if (ovlName == NULL)
fprintf(stderr, "ERROR: No overlap store (-O) supplied.\n");
if ((maxJob == 0) && (doExplicitTest == false))
fprintf(stderr, "ERROR: One of -F (number of slices) or -t (test a store) must be supplied.\n");
exit(1);
}
// Do the test, and maybe fix things up.
if (doExplicitTest == true) {
bool passed = testIndex(ovlName, doFixes);
exit((passed == true) ? 0 : 1);
}
// Check that all segments are present. Every segment should have an info file.
uint32 cntJob = 0;
for (uint32 i=1; i<=maxJob; i++) {
uint32 complete = 0;
sprintf(name, "%s/%04d", ovlName, i);
if (AS_UTL_fileExists(name, FALSE, FALSE) == true)
complete++;
else
fprintf(stderr, "ERROR: Segment "F_U32" data not present (%s)\n", i, name);
sprintf(name, "%s/%04d.info", ovlName, i);
if (AS_UTL_fileExists(name, FALSE, FALSE) == true)
complete++;
else
fprintf(stderr, "ERROR: Segment "F_U32" info not present (%s)\n", i, name);
sprintf(name, "%s/%04d.index", ovlName, i);
if (AS_UTL_fileExists(name, FALSE, FALSE) == true)
complete++;
else
fprintf(stderr, "ERROR: Segment "F_U32" index not present (%s)\n", i, name);
if (complete == 3)
cntJob++;
}
if (cntJob != maxJob) {
fprintf(stderr, "ERROR: Expected "F_U32" segments, only found "F_U32".\n", maxJob, cntJob);
exit(1);
}
// Merge the stuff.
mergeInfoFiles(ovlName, maxJob);
// Diagnostics.
if (testIndex(ovlName, false) == false) {
fprintf(stderr, "ERROR: index failed tests.\n");
exit(1);
}
// Remove intermediates. For the buckets, we keep going until there are 10 in a row not present.
// During testing, on a microbe using 2850 buckets, some buckets were empty.
if (deleteIntermediates == false) {
fprintf(stderr, "\n");
fprintf(stderr, "Not removing intermediate files. Finished.\n");
exit(0);
}
fprintf(stderr, "\n");
fprintf(stderr, "Removing intermediate files.\n");
// Removing indices is easy, beacuse we know how many there are.
for (uint32 i=1; i<=maxJob; i++) {
sprintf(name, "%s/%04u.index", ovlName, i);
AS_UTL_unlink(name);
sprintf(name, "%s/%04u.info", ovlName, i);
AS_UTL_unlink(name);
}
// We don't know how many buckets there are, so we remove until we fail to find ten
// buckets in a row.
for (uint32 missing=0, i=1; missing<10; i++) {
sprintf(name, "%s/bucket%04d", ovlName, i);
if (AS_UTL_fileExists(name, TRUE, FALSE) == FALSE) {
missing++;
continue;
}
missing = 0;
sprintf(name, "%s/bucket%04d/sliceSizes", ovlName, i);
AS_UTL_unlink(name);
sprintf(name, "%s/bucket%04d", ovlName, i);
rmdir(name);
}
fprintf(stderr, "Finished.\n");
exit(0);
}
int main() {
if(testIndex("FORTRAN","R",3))
return 1;
if(testIndex("FORTRAN","R",5,true))
return 1;
if(testIndex("hello","ell",2))
return 1;
if(testIndex("hello","ell",2,true))
return 1;
if(testIndex("hello","world",0))
return 1;
if(testIndex("hello","world",0,true))
return 1;
if(testIndex("A","a",0))
return 1;
if(testIndex("hell","hello",0))
return 1;
if(testIndex("hell","hello",0,true))
return 1;
if(testIndex("hello","",1))
return 1;
if(testIndex("hello","",6,true))
return 1;
return 0;
}