rc_t CC KMain(int argc, char *argv[])
{
static const char *help[] = { "--help", "-h", "-?", NULL };
static const char *vers[] = { "--version", "-V", NULL };
bool const has_help = has_arg(help, argc, argv);
bool const has_vers = has_arg(vers, argc, argv);
XMLLogger const *logger = NULL;
int argfirst = 0;
int arglast = 0;
rc_t rc = 0;
unsigned load = 0;
if (has_help) {
argc = 2;
argv[1] = "--help";
return main_help_vers(argc, argv);
}
if (has_vers) {
argc = 2;
argv[1] = "--version";
return main_help_vers(argc, argv);
}
logger = make_logger(&argc, argv);
memset(&G, 0, sizeof(G));
G.mode = mode_Archive;
G.globalMode = mode_Archive;
G.maxSeqLen = TableWriterRefSeq_MAX_SEQ_LEN;
G.schemaPath = strdup(SCHEMAFILE);
G.omit_aligned_reads = true;
G.omit_reference_reads = true;
G.minMapQual = 0; /* accept all */
G.tmpfs = strdup("/tmp");
G.cache_size = ((size_t)16) << 30;
G.maxErrCount = 1000;
G.minMatchCount = 10;
set_pid();
for (arglast = 1; arglast < argc; ++arglast) {
if (strcmp(argv[arglast], "--remap") == 0) {
argv[arglast] = argv[0];
G.globalMode = mode_Remap;
rc = main_1(arglast - argfirst, argv + argfirst, true, load);
if (rc)
break;
G.mode = mode_Remap;
argfirst = arglast;
++load;
}
}
rc = main_1(arglast - argfirst, argv + argfirst, false, load);
XMLLogger_Release(logger);
cleanupGlobal();
return rc;
}
rc_t CC KMain (int argc, char * argv[])
{
Args * args;
rc_t rc;
unsigned n_aligned = 0;
unsigned n_unalgnd = 0;
char *aligned[256];
char *unalgnd[256];
char *name_buffer = NULL;
unsigned next_name = 0;
unsigned nbsz = 0;
char const *value;
char *dummy;
const XMLLogger* xml_logger = NULL;
memset(&G, 0, sizeof(G));
G.mode = mode_Archive;
G.maxSeqLen = TableWriterRefSeq_MAX_SEQ_LEN;
G.schemaPath = SCHEMAFILE;
G.omit_aligned_reads = true;
G.omit_reference_reads = true;
G.minMapQual = 0; /* accept all */
G.tmpfs = "/tmp";
#if _ARCH_BITS == 32
G.cache_size = ( size_t ) 1 << 30;
#else
G.cache_size = ( size_t ) 10 << 30;
#endif
G.maxErrCount = 1000;
G.minMatchCount = 10;
set_pid();
rc = ArgsMakeAndHandle (&args, argc, argv, 2, Options,
sizeof Options / sizeof (OptDef), XMLLogger_Args, XMLLogger_ArgsQty);
while (rc == 0) {
uint32_t pcount;
if( (rc = XMLLogger_Make(&xml_logger, NULL, args)) != 0 ) {
break;
}
rc = ArgsOptionCount(args, option_only_verify, &pcount);
if (rc)
break;
G.onlyVerifyReferences = (pcount > 0);
rc = ArgsOptionCount(args, option_no_verify, &pcount);
if (rc)
break;
G.noVerifyReferences = (pcount > 0);
rc = ArgsOptionCount(args, option_use_qual, &pcount);
if (rc)
break;
G.useQUAL = (pcount > 0);
rc = ArgsOptionCount(args, option_ref_config, &pcount);
if (rc)
break;
G.limit2config = (pcount > 0);
rc = ArgsOptionCount(args, OPTION_REF_FILE, &pcount);
if (rc)
break;
G.refFiles = calloc(pcount + 1, sizeof(*(G.refFiles)));
if( !G.refFiles ) {
rc = RC(rcApp, rcArgv, rcAccessing, rcMemory, rcExhausted);
break;
}
while(pcount-- > 0) {
rc = ArgsOptionValue(args, OPTION_REF_FILE, pcount, &G.refFiles[pcount]);
if (rc)
break;
}
rc = ArgsOptionCount (args, OPTION_TMPFS, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_TMPFS, 0, &G.tmpfs);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_INPUT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_INPUT, 0, &G.inpath);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single input parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, option_ref_filter, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, option_ref_filter, 0, &G.refFilter);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_CONFIG, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_CONFIG, 0, &G.refXRefPath);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single input parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_OUTPUT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_OUTPUT, 0, &G.outpath);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single output parameter required\n"));
MiniUsage (args);
break;
}
else if (!G.onlyVerifyReferences) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcInsufficient);
OUTMSG (("Output parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_MINMAPQ, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MINMAPQ, 0, &value);
if (rc)
break;
G.minMapQual = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_QCOMP, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_QCOMP, 0, &G.QualQuantizer);
if (rc)
break;
}
rc = ArgsOptionCount (args, option_edit_aligned_qual, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, option_edit_aligned_qual, 0, &value);
if (rc)
break;
G.alignedQualValue = strtoul(value, &dummy, 0);
if (G.alignedQualValue == 0) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcIncorrect);
OUTMSG (("edit-aligned-qual: bad value\n"));
MiniUsage (args);
break;
}
G.editAlignedQual = true;
}
rc = ArgsOptionCount (args, OPTION_CACHE_SIZE, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_CACHE_SIZE, 0, &value);
if (rc)
break;
G.cache_size = strtoul(value, &dummy, 0) * 1024UL * 1024UL;
if (G.cache_size == 0) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcIncorrect);
OUTMSG (("cache-size: bad value\n"));
MiniUsage (args);
break;
}
}
rc = ArgsOptionCount (args, OPTION_MAX_WARN_DUP_FLAG, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_WARN_DUP_FLAG, 0, &value);
if (rc)
break;
G.maxWarnCount_DupConflict = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, option_unsorted, &pcount);
if (rc)
break;
G.expectUnsorted = pcount > 0;
rc = ArgsOptionCount (args, OPTION_MAX_REC_COUNT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_REC_COUNT, 0, &value);
if (rc)
break;
G.maxAlignCount = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_MAX_ERR_COUNT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_ERR_COUNT, 0, &value);
if (rc)
break;
G.maxErrCount = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_MIN_MATCH, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MIN_MATCH, 0, &value);
if (rc)
break;
G.minMatchCount = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_ACCEPT_DUP, &pcount);
if (rc)
break;
G.acceptBadDups = pcount > 0;
rc = ArgsOptionCount (args, OPTION_ACCEPT_NOMATCH, &pcount);
if (rc)
break;
G.acceptNoMatch = pcount > 0;
rc = ArgsOptionCount (args, option_keep_mismatch_qual, &pcount);
if (rc)
break;
G.keepMismatchQual = pcount > 0;
rc = ArgsOptionCount (args, OPTION_NO_CS, &pcount);
if (rc)
break;
G.noColorSpace = pcount > 0;
rc = ArgsOptionCount (args, OPTION_NO_SECONDARY, &pcount);
if (rc)
break;
G.noSecondary = pcount > 0;
rc = ArgsOptionCount (args, OPTION_TI, &pcount);
if (rc)
break;
G.hasTI = pcount > 0;
rc = ArgsOptionCount (args, OPTION_ACCEPT_HARD_CLIP, &pcount);
if (rc)
break;
G.acceptHardClip = pcount > 0;
rc = ArgsOptionCount (args, OPTION_NOMATCH_LOG, &pcount);
if (rc)
break;
if (pcount == 1)
{
KDirectory *dir;
rc = ArgsOptionValue (args, OPTION_NOMATCH_LOG, 0, &value);
if (rc) break;
rc = KDirectoryNativeDir(&dir);
if (rc) break;
rc = KDirectoryCreateFile(dir, &G.noMatchLog, 0, 0664, kcmInit, value);
KDirectoryRelease(dir);
if (rc) break;
}
rc = ArgsOptionCount (args, OPTION_HEADER, &pcount);
if (rc)
break;
if (pcount == 1) {
rc = ArgsOptionValue (args, OPTION_HEADER, 0, &value);
if (rc) break;
rc = LoadHeader(&G.headerText, value, G.inpath);
if (rc) break;
}
rc = ArgsParamCount (args, &pcount);
if (rc) break;
if (pcount == 0)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcInsufficient);
MiniUsage (args);
break;
}
else if (pcount > sizeof(aligned)/sizeof(aligned[0])) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
(void)PLOGERR(klogErr, (klogErr, rc, "$(count) input files is too many, $(max) is the limit",
"count=%u,max=%u", (unsigned)pcount, (unsigned)(sizeof(aligned)/sizeof(aligned[0]))));
break;
}
else {
unsigned need = G.inpath ? (strlen(G.inpath) + 1) * pcount : 0;
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsParamValue(args, i, &value);
if (rc) break;
need += strlen(value) + 1;
}
nbsz = need;
}
rc = ArgsOptionCount (args, OPTION_UNALIGNED, &pcount);
if (rc)
break;
if (pcount > 0)
{
unsigned need = G.inpath ? (strlen(G.inpath) + 1) * pcount : 0;
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsOptionValue(args, OPTION_UNALIGNED, i, &value);
if (rc) break;
need += strlen(value) + 1;
}
if (rc) break;
nbsz += need;
}
name_buffer = malloc(nbsz);
if (name_buffer == NULL) {
rc = RC(rcApp, rcArgv, rcAccessing, rcMemory, rcExhausted);
break;
}
rc = ArgsOptionCount (args, OPTION_UNALIGNED, &pcount);
if (rc == 0) {
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsOptionValue(args, OPTION_UNALIGNED, i, &value);
if (rc) break;
unalgnd[n_unalgnd++] = name_buffer + next_name;
rc = PathWithBasePath(name_buffer + next_name, nbsz - next_name, value, G.inpath);
if (rc) break;
next_name += strlen(name_buffer + next_name) + 1;
}
if (rc) break;
}
else
break;
rc = ArgsParamCount (args, &pcount);
if (rc == 0) {
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsParamValue(args, i, &value);
if (rc) break;
aligned[n_aligned++] = name_buffer + next_name;
rc = PathWithBasePath(name_buffer + next_name, nbsz - next_name, value, G.inpath);
if (rc) break;
next_name += strlen(name_buffer + next_name) + 1;
}
}
else
break;
rc = run(argv[0], n_aligned, (char const **)aligned, n_unalgnd, (char const **)unalgnd);
break;
}
free(name_buffer);
free((void *)G.headerText);
free(G.refFiles);
value = G.outpath ? strrchr(G.outpath, '/') : "/???";
if( value == NULL ) {
value = G.outpath;
} else {
value++;
}
if (rc) {
(void)PLOGERR(klogErr, (klogErr, rc, "load failed",
"severity=total,status=failure,accession=%s,errors=%u", value, G.errCount));
} else {
(void)PLOGMSG(klogInfo, (klogInfo, "loaded",
"severity=total,status=success,accession=%s,errors=%u", value, G.errCount));
}
ArgsWhack(args);
XMLLogger_Release(xml_logger);
return rc;
}
rc_t CC KMain( int argc, char* argv[] )
{
rc_t rc = 0;
Args* args = NULL;
const char* errmsg = NULL, *refseq_chunk = NULL, *min_mapq = NULL, *cluster_size = NULL;
const XMLLogger* xml_logger = NULL;
SParam params;
memset(¶ms, 0, sizeof(params));
params.schema = "align/align.vschema";
params.argv0 = argv[0];
if( (rc = ArgsMakeAndHandle(&args, argc, argv, 2, MainArgs, MainArgsQty, XMLLogger_Args, XMLLogger_ArgsQty)) == 0 ) {
uint32_t count;
if( (rc = ArgsParamCount (args, &count)) != 0 || count != 0 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
ArgsParamValue(args, 0, &errmsg);
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_Output].name, &count)) != 0 || count != 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, count ? rcExcessive : rcInsufficient);
errmsg = MainArgs[eopt_Output].name;
} else if( (rc = ArgsOptionValue(args, MainArgs[eopt_Output].name, 0, ¶ms.out)) != 0 ) {
errmsg = MainArgs[eopt_Output].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_MapInput].name, &count)) != 0 || count != 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, count ? rcExcessive : rcInsufficient);
errmsg = MainArgs[eopt_MapInput].name;
} else if( (rc = ArgsOptionValue(args, MainArgs[eopt_MapInput].name, 0, ¶ms.map_path)) != 0 ) {
errmsg = MainArgs[eopt_MapInput].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_Schema].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, count ? rcExcessive : rcInsufficient);
errmsg = MainArgs[eopt_Schema].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_Schema].name, 0, ¶ms.schema)) != 0 ) {
errmsg = MainArgs[eopt_Schema].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_AsmInput].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_AsmInput].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_AsmInput].name, 0, ¶ms.asm_path)) != 0 ) {
errmsg = MainArgs[eopt_AsmInput].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_RefSeqConfig].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_RefSeqConfig].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_RefSeqConfig].name, 0, ¶ms.refseqcfg)) != 0 ) {
errmsg = MainArgs[eopt_RefSeqConfig].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_RefSeqPath].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_RefSeqPath].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_RefSeqPath].name, 0, ¶ms.refseqpath)) != 0 ) {
errmsg = MainArgs[eopt_RefSeqPath].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_Library].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_Library].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_Library].name, 0, ¶ms.library)) != 0 ) {
errmsg = MainArgs[eopt_Library].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_RefSeqChunk].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_RefSeqChunk].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_RefSeqChunk].name, 0, &refseq_chunk)) != 0 ) {
errmsg = MainArgs[eopt_RefSeqChunk].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_Force].name, ¶ms.force)) != 0 ) {
errmsg = MainArgs[eopt_Force].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_ForceRef].name, ¶ms.force_refw)) != 0 ) {
errmsg = MainArgs[eopt_ForceRef].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_ForceRead].name, ¶ms.force_readw)) != 0 ) {
errmsg = MainArgs[eopt_ForceRead].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_noReadAhead].name, ¶ms.no_read_ahead)) != 0 ) {
errmsg = MainArgs[eopt_noReadAhead].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_NoSpotGroup].name, ¶ms.no_spot_group)) != 0 ) {
errmsg = MainArgs[eopt_NoSpotGroup].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_No2nd_ary].name, ¶ms.min_mapq)) != 0 ) {
errmsg = MainArgs[eopt_No2nd_ary].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_QualQuantization].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_QualQuantization].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_QualQuantization].name, 0, ¶ms.qual_quant)) != 0 ) {
errmsg = MainArgs[eopt_QualQuantization].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_MinMapQ].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_MinMapQ].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_MinMapQ].name, 0, &min_mapq)) != 0 ) {
errmsg = MainArgs[eopt_MinMapQ].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_ClusterSize].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_ClusterSize].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_ClusterSize].name, 0, &cluster_size)) != 0 ) {
errmsg = MainArgs[eopt_ClusterSize].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_SingleMate].name, ¶ms.single_mate)) != 0 ) {
errmsg = MainArgs[eopt_SingleMate].name;
} else {
do {
long val = 0;
char* end = NULL;
uint32_t count;
if( (rc = ArgsOptionCount(args, MainArgs[eopt_RefFile].name, &count)) != 0 ) {
break;
} else {
params.refFiles = calloc(count + 1, sizeof(*(params.refFiles)));
if( params.refFiles == NULL ) {
rc = RC(rcApp, rcArgv, rcReading, rcMemory, rcExhausted);
break;
}
while(rc == 0 && count-- > 0) {
rc = ArgsOptionValue(args, MainArgs[eopt_RefFile].name, count, ¶ms.refFiles[count]);
}
}
if( refseq_chunk != NULL ) {
errno = 0;
val = strtol(refseq_chunk, &end, 10);
if( errno != 0 || refseq_chunk == end || *end != '\0' || val < 0 || val > UINT32_MAX ) {
rc = RC(rcExe, rcArgv, rcReading, rcParam, rcInvalid);
break;
}
params.refseq_chunk = val;
}
if( params.min_mapq > 0 ) {
params.min_mapq = ~0;
} else if( min_mapq != NULL ) {
errno = 0;
val = strtol(min_mapq, &end, 10);
if( errno != 0 || min_mapq == end || *end != '\0' || val < 0 || val > 255 ) {
rc = RC(rcExe, rcArgv, rcReading, rcParam, rcInvalid);
break;
}
params.min_mapq = val;
}
if ( cluster_size )
params.cluster_size = atoi( cluster_size );
else
params.cluster_size = 0;
rc = KDirectoryNativeDir( ¶ms.input_dir );
if ( rc != 0 )
errmsg = "current directory";
else
{
rc = XMLLogger_Make( &xml_logger, params.input_dir, args );
if ( rc != 0 )
errmsg = "XML logging";
else
rc = Load( ¶ms );
}
} while( false );
KDirectoryRelease( params.input_dir );
}
}
/* find accession as last part of path for internal XML logging */
refseq_chunk = params.out ? strrchr(params.out, '/') : "/???";
if( refseq_chunk ++ == NULL )
refseq_chunk = params.out;
if( argc < 2 )
MiniUsage(args);
else if( rc != 0 )
{
if( errmsg )
{
MiniUsage(args);
LOGERR(klogErr, rc, errmsg);
}
else
{
PLOGERR(klogErr, (klogErr, rc, "load failed: $(reason_short)",
"severity=total,status=failure,accession=%s", refseq_chunk));
}
}
else
{
PLOGMSG(klogInfo, (klogInfo, "loaded",
"severity=total,status=success,accession=%s", refseq_chunk));
}
ArgsWhack(args);
XMLLogger_Release(xml_logger);
return rc;
}
LIB_EXPORT rc_t CC XMLLogger_Make2(const XMLLogger** self, KDirectory* dir, const char* logpath, const int fd)
{
rc_t rc = 0;
XMLLogger* obj;
KDirectory* my_dir = NULL;
const uint32_t lopt = klogFmtTimestamp | klogFmtSeverity |
klogFmtMessage | klogFmtAppName | klogFmtAppVersion | klogFmtReasonShort;
const uint32_t sopt = kstsFmtTimestamp | kstsFmtMessage | kstsFmtAppName | kstsFmtAppVersion;
KLogFmtFlagsSet(lopt);
KLogLibFmtFlagsSet(lopt);
KStsFmtFlagsSet(sopt);
KStsLibFmtFlagsSet(sopt);
obj = calloc(1, sizeof(*obj));
if( obj == NULL ) {
rc = RC(rcApp, rcLog, rcAllocating, rcMemory, rcExhausted);
} else if( fd < 0 && dir == NULL && (rc = KDirectoryNativeDir(&my_dir)) != 0 ) {
} else if( fd >= 0 && (rc = KFileMakeFDFileWrite(&obj->file.file, false, fd)) != 0 ) {
} else if( logpath != NULL && fd < 0 && (rc = KDirectoryCreateFile(dir ? dir : my_dir, &obj->file.file, false, 0644, kcmInit, "%s", logpath)) != 0 ) {
} else {
obj->file.pos = 0;
obj->log.file = &obj->file;
obj->log.fmt.formatter = KLogFmtWriterGet();
obj->log.fmt.data = KLogFmtDataGet();
obj->log.wrt.writer = KLogWriterGet();
obj->log.wrt.data = KLogDataGet();
obj->loglib.file = &obj->file;
obj->loglib.fmt.formatter = KLogLibFmtWriterGet();
obj->loglib.fmt.data = KLogLibFmtDataGet();
obj->loglib.wrt.writer = KLogLibWriterGet();
obj->loglib.wrt.data = KLogLibDataGet();
obj->sts.file = &obj->file;
obj->sts.fmt.formatter = KStsFmtWriterGet();
obj->sts.fmt.data = KStsFmtDataGet();
obj->sts.wrt.writer = KStsWriterGet();
obj->sts.wrt.data = KStsDataGet();
obj->stslib.file = &obj->file;
obj->stslib.fmt.formatter = KStsLibFmtWriterGet();
obj->stslib.fmt.data = KStsLibFmtDataGet();
obj->stslib.wrt.writer = KStsLibWriterGet();
obj->stslib.wrt.data = KStsLibDataGet();
if( (rc = KLogFmtHandlerSet(LoaderXMLFormatter, lopt, &obj->log)) == 0 &&
(rc = KLogLibFmtHandlerSet(LoaderXMLFormatter, lopt, &obj->loglib)) == 0 &&
(rc = KStsFmtHandlerSet(LoaderXMLFormatter, sopt, &obj->sts)) == 0 &&
(rc = KStsLibFmtHandlerSet(LoaderXMLFormatter, sopt, &obj->stslib)) == 0 ) {
/* make log valid XML */
if( obj->file.file != NULL ) {
size_t num_writ = 0;
rc = KFileWrite(obj->file.file, obj->file.pos, "<Log>\n", 6, &num_writ);
obj->file.pos += num_writ;
}
}
}
KDirectoryRelease(my_dir);
if( rc == 0 ) {
*self = obj;
if( fd >= 0 ) {
DBG(("XML Log file set to handle %d\n", fd));
} else if( logpath != NULL) {
DBG(("XML Log file set to %s\n", logpath));
}
} else {
XMLLogger_Release(obj);
*self = NULL;
}
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
XMLLogger const *xlogger = NULL;
Args * args;
rc_t rc;
bool any_failed = false;
CheckCorruptConfig config = { -1.0, SA_TABLE_LOOKUP_LIMIT, -1.0, SEQ_TABLE_LOOKUP_LIMIT, PA_LONGER_SA_LIMIT, 0 };
KLogLevelSet(klogInfo);
rc = ArgsMakeAndHandle (&args, argc, argv, 2, Options,
sizeof (Options) / sizeof (Options[0]),
XMLLogger_Args, XMLLogger_ArgsQty);
if (rc)
LOGERR (klogInt, rc, "failed to parse command line parameters");
else
{
rc = XMLLogger_Make(&xlogger, NULL, args);
if (rc)
LOGERR (klogInt, rc, "failed to make xml logger");
else
{
rc = parseArgs ( args, &config );
if (rc == 0)
{
uint32_t pcount;
rc = ArgsParamCount ( args, &pcount );
if (rc)
LOGERR (klogInt, rc, "ArgsParamCount() failed");
else
{
if ( pcount == 0 )
LOGMSG (klogErr, "no accessions were passed in");
else
{
for ( uint32_t i = 0; i < pcount; ++i )
{
const char * accession;
rc = ArgsParamValue ( args, i, (const void **)&accession );
if (rc)
{
PLOGERR (klogInt, (klogInt, rc, "failed to get $(PARAM_I) accession from command line", "PARAM_I=%d", i));
any_failed = true;
}
else
{
if (!checkAccession ( accession, &config ))
any_failed = true;
}
}
if (!any_failed)
LOGMSG (klogInfo, "All accessions are good!");
}
}
}
XMLLogger_Release(xlogger);
}
ArgsWhack ( args );
}
return rc != 0 || any_failed ? 1 : 0;
}
rc_t CC KMain (int argc, char * argv[])
{
Args * args;
rc_t rc;
char *files[256];
int8_t defaultReadNumbers[256];
char *name_buffer = NULL;
size_t next_name = 0;
size_t nbsz = 0;
char const *value;
char *dummy;
const XMLLogger* xml_logger = NULL;
enum FASTQQualityFormat qualityFormat;
bool ignoreSpotGroups;
memset(&G, 0, sizeof(G));
G.mode = mode_Archive;
G.maxSeqLen = TableWriterRefSeq_MAX_SEQ_LEN;
G.schemaPath = SCHEMAFILE;
G.omit_aligned_reads = true;
G.omit_reference_reads = true;
G.minMapQual = 0; /* accept all */
G.tmpfs = "/tmp";
#if _ARCH_BITS == 32
G.cache_size = ( size_t ) 1 << 30;
#else
G.cache_size = ( size_t ) 10 << 30;
#endif
G.maxErrCount = 1000;
G.maxErrPct = 5;
G.acceptNoMatch = true;
G.minMatchCount = 0;
G.QualQuantizer="0";
set_pid();
rc = ArgsMakeAndHandle (&args, argc, argv, 2, Options,
sizeof Options / sizeof (OptDef), XMLLogger_Args, XMLLogger_ArgsQty);
while (rc == 0) {
uint32_t pcount;
if( (rc = XMLLogger_Make(&xml_logger, NULL, args)) != 0 ) {
break;
}
rc = ArgsOptionCount (args, OPTION_TMPFS, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_TMPFS, 0, (const void **)&G.tmpfs);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_OUTPUT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_OUTPUT, 0, (const void **)&G.outpath);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single output parameter required\n"));
MiniUsage (args);
break;
}
else {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcInsufficient);
OUTMSG (("Output parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_QCOMP, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_QCOMP, 0, (const void **)&G.QualQuantizer);
if (rc)
break;
}
rc = ArgsOptionCount (args, OPTION_CACHE_SIZE, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_CACHE_SIZE, 0, (const void **)&value);
if (rc)
break;
G.cache_size = strtoul(value, &dummy, 0) * 1024UL * 1024UL;
if (G.cache_size == 0 || G.cache_size == ULONG_MAX) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcIncorrect);
OUTMSG (("cache-size: bad value\n"));
MiniUsage (args);
break;
}
}
G.expectUnsorted = true;
rc = ArgsOptionCount (args, OPTION_MAX_REC_COUNT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_REC_COUNT, 0, (const void **)&value);
if (rc)
break;
G.maxAlignCount = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_MAX_ERR_COUNT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_ERR_COUNT, 0, (const void **)&value);
if (rc)
break;
G.maxErrCount = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_MAX_ERR_PCT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_ERR_PCT, 0, (const void **)&value);
if (rc)
break;
G.maxErrPct = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_PLATFORM, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_PLATFORM, 0, (const void **)&value);
if (rc)
break;
G.platform = PlatformToId(value);
if (G.platform == SRA_PLATFORM_UNDEFINED)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcIncorrect);
(void)PLOGERR(klogErr, (klogErr, rc, "Invalid platform $(v)",
"v=%s", value));
break;
}
}
else
G.platform = SRA_PLATFORM_UNDEFINED;
rc = ArgsOptionCount (args, OPTION_QUALITY, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_QUALITY, 0, (const void **)&value);
if (rc)
break;
if (strcmp(value, "PHRED_33") == 0)
qualityFormat = FASTQphred33;
else if (strcmp(value, "PHRED_64") == 0)
qualityFormat = FASTQphred64;
else if (strcmp(value, "LOGODDS") == 0)
qualityFormat = FASTQlogodds;
else
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcIncorrect);
(void)PLOGERR(klogErr, (klogErr, rc, "Invalid quality encoding $(v)",
"v=%s", value));
break;
}
}
else
qualityFormat = 0;
rc = ArgsOptionCount (args, OPTION_IGNORE_ILLUMINA_TAGS, &pcount);
if (rc)
break;
ignoreSpotGroups = pcount > 0;
rc = ArgsParamCount (args, &pcount);
if (rc) break;
if (pcount == 0)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcInsufficient);
MiniUsage (args);
break;
}
else if (pcount > sizeof(files)/sizeof(files[0])) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
(void)PLOGERR(klogErr, (klogErr, rc, "$(count) input files is too many, $(max) is the limit",
"count=%u,max=%u", (unsigned)pcount, (unsigned)(sizeof(files)/sizeof(files[0]))));
break;
}
else {
size_t need = G.inpath ? (strlen(G.inpath) + 1) * pcount : 0;
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsParamValue(args, i, (const void **)&value);
if (rc) break;
need += strlen(value) + 1;
}
nbsz = need;
}
name_buffer = malloc(nbsz);
if (name_buffer == NULL) {
rc = RC(rcApp, rcArgv, rcAccessing, rcMemory, rcExhausted);
break;
}
rc = ArgsParamCount (args, &pcount);
if (rc == 0) {
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsParamValue(args, i, (const void **)&value);
if (rc) break;
defaultReadNumbers[i] = 0;
files[i] = name_buffer + next_name;
rc = PathWithBasePath(name_buffer + next_name, nbsz - next_name, value, G.inpath);
if (rc) break;
next_name += strlen(name_buffer + next_name) + 1;
}
}
else
break;
rc = run(argv[0], &G, pcount, (char const **)files, qualityFormat, defaultReadNumbers, ignoreSpotGroups);
break;
}
free(name_buffer);
value = G.outpath ? strrchr(G.outpath, '/') : "/???";
if( value == NULL ) {
value = G.outpath;
} else {
value++;
}
if (rc) {
(void)PLOGERR(klogErr, (klogErr, rc, "load failed",
"severity=total,status=failure,accession=%s,errors=%u", value, G.errCount));
} else {
(void)PLOGMSG(klogInfo, (klogInfo, "loaded",
"severity=total,status=success,accession=%s,errors=%u", value, G.errCount));
}
ArgsWhack(args);
XMLLogger_Release(xml_logger);
return rc;
}
