本文整理汇总了C++中RC函数的典型用法代码示例。如果您正苦于以下问题：C++ RC函数的具体用法？C++ RC怎么用？C++ RC使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了RC函数的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: matcher_execute
rc_t matcher_execute( matcher* self, const p_matcher_input in )
{
VSchema * dflt_schema;
const VTable * src_table;
rc_t rc;
if ( self == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcSelf, rcNull );
if ( in->manager == NULL || in->add_schemas == NULL ||
in->cfg == NULL || in->columns == NULL ||
in->src_path == NULL || in->dst_path == NULL ||
in->dst_tabname == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcParam, rcNull );
rc = matcher_build_column_vector( self, in->columns );
if ( rc != 0 ) return rc;
rc = matcher_exclude_columns( self, in->excluded_columns );
if ( rc != 0 ) return rc;
rc = helper_parse_schema( in->manager, &dflt_schema, in->add_schemas );
if ( rc != 0 ) return rc;
rc = VDBManagerOpenTableRead( in->manager, &src_table, dflt_schema, "%s", in->src_path );
if ( rc == 0 )
{
const VSchema * src_schema;
rc = VTableOpenSchema ( src_table, &src_schema );
if ( rc == 0 )
{
rc = matcher_read_src_types( self, src_table, src_schema );
if ( rc == 0 )
{
if ( in->legacy_schema != NULL )
rc = VSchemaParseFile ( dflt_schema, "%s", in->legacy_schema );
if ( rc == 0 )
{
VTable * dst_table;
KCreateMode cmode = kcmParents;
const VSchema * dst_schema = src_schema;
if ( in->legacy_schema != NULL )
dst_schema = dflt_schema;
if ( in->force_unlock )
VDBManagerUnlock ( in->manager, "%s", in->dst_path );
if ( in->force_kcmInit )
cmode |= kcmInit;
else
cmode |= kcmCreate;
rc = VDBManagerCreateTable( in->manager, &dst_table,
dst_schema, in->dst_tabname, cmode, "%s", in->dst_path );
if ( rc == 0 )
{
rc = matcher_read_dst_types( self, dst_table, dst_schema );
if ( rc == 0 )
{
rc = matcher_make_type_matrix( self );
if ( rc == 0 )
rc = matcher_match_matrix( self, src_schema, in->cfg );
}
VTableRelease( dst_table );
if ( !(in->force_kcmInit) )
KDirectoryRemove ( in->dir, true, "%s", in->dst_path );
}
}
}
VSchemaRelease( src_schema );
}
VTableRelease( src_table );
}
VSchemaRelease( dflt_schema );
return rc;
}示例2: MakeIndexes
static
rc_t MakeIndexes(const SRATable* stbl, KTable* ktbl, KMetadata* meta)
{
rc_t rc = 0;
int i;
char* buffer = NULL;
size_t buffer_sz = g_file_block_sz * 100;
SIndexObj idx[] = {
/* meta, file, format, index, func, file_size, buffer_sz, minSpotId, maxSpotId */
{NULL, "fastq", "fastq", "fuse-fastq", Fastq_Idx, 0, 0, 0, 0},
{NULL, "sff", "SFF", "fuse-sff", SFF_Idx, 0, 0, 0, 0},
{NULL, "fastq.gz", "fastq-gzip", "fuse-fastq-gz", FastqGzip_Idx, 0, 0, 0, 0},
{NULL, "sff.gz", "SFF-gzip", "fuse-sff-gz", SFFGzip_Idx, 0, 0, 0, 0}
};
for(i = 0; rc == 0 && i < sizeof(idx) / sizeof(idx[0]); i++) {
KMDataNode* parent = NULL;
if( (rc = KMetadataOpenNodeUpdate(meta, &parent, "/FUSE")) == 0 ) {
KMDataNodeDropChild(parent, "root"); /* drop old stuff */
if( g_ungzip || strcmp(&idx[i].file[strlen(idx[i].file) - 3], ".gz") == 0 ) {
STSMSG(0, ("Preparing index %s", idx[i].index));
MD5StateInit(&idx[i].md5);
SLListInit(&idx[i].li);
KMDataNodeDropChild(parent, "%s.tmp", idx[i].file);
if( (rc = KMDataNodeOpenNodeUpdate(parent, &idx[i].meta, "%s.tmp", idx[i].file)) == 0 ) {
if( idx[i].func != NULL ) {
if( buffer == NULL ) {
if( (buffer = malloc(buffer_sz)) == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
break;
}
}
rc = idx[i].func(stbl, &idx[i], buffer, buffer_sz);
if( rc == 0 ) {
MD5StateFinish(&idx[i].md5, idx[i].md5_digest);
rc = CommitIndex(ktbl, idx[i].index, &idx[i].li);
}
}
if( rc == 0 ) {
rc = WriteFileMeta(&idx[i]);
}
KMDataNodeRelease(idx[i].meta);
}
if( GetRCState(rc) == rcUnsupported ) {
KMDataNodeDropChild(parent, "%s", idx[i].file);
PLOGERR(klogWarn, (klogWarn, rc, "Index $(i) is not supported for this table", PLOG_S(i), idx[i].index));
rc = 0;
} else if( rc == 0 ) {
char f[4096];
strcpy(f, idx[i].file);
strcat(f, ".tmp");
KMDataNodeDropChild(parent, "%s", idx[i].file);
rc = KMDataNodeRenameChild(parent, f, idx[i].file);
}
} else if( !g_ungzip ) {
KTableDropIndex(ktbl, idx[i].index);
KMDataNodeDropChild(parent, "%s", idx[i].file);
}
KMDataNodeDropChild(parent, "%s.tmp", idx[i].file);
KMDataNodeRelease(parent);
}
SLListWhack(&idx[i].li, WhackIndexData, NULL);
}
free(buffer);
return rc;
}示例3: SFF_Idx
static
rc_t SFF_Idx(const SRATable* sratbl, SIndexObj* obj, char* buffer, const size_t buffer_sz)
{
rc_t rc = 0;
const SFFReader* reader = NULL;
if( (rc = SFFReaderMake(&reader, sratbl, g_accession, obj->minSpotId, obj->maxSpotId)) != 0 ) {
return rc;
} else {
size_t written = 0;
uint32_t blk = 0;
SIndexNode* inode = NULL;
while( rc == 0 ) {
rc = SFFReader_GetNextSpotData(reader, buffer, buffer_sz, &written);
if( blk >= g_file_block_sz || (GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted) ) {
inode->key_size = blk;
SLListPushTail(&obj->li, &inode->n);
DEBUG_MSG(5, ("SFF index closed spots %lu, offset %lu, block size %lu\n", inode->id_qty, inode->key, inode->key_size));
inode = NULL;
if( blk > obj->buffer_sz ) {
obj->buffer_sz = blk;
}
blk = 0;
}
if( GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted ) {
rc = 0;
break;
}
if( inode == NULL ) {
spotid_t spotid = 0;
if( (rc = SFFReaderCurrentSpot(reader, &spotid)) != 0 ) {
break;
}
inode = malloc(sizeof(SIndexNode));
if( inode == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
break;
}
inode->key = obj->file_size;
inode->key_size = 0;
inode->id = spotid;
inode->id_qty = 0;
DEBUG_MSG(5, ("SFF index opened spot %ld, offset %lu\n", inode->id, inode->key));
if( spotid == 1 ) {
char hd[10240];
size_t hd_sz = 0;
if( (rc = SFFReaderHeader(reader, 0, hd, sizeof(hd), &hd_sz)) == 0 ) {
obj->file_size += hd_sz;
blk += hd_sz;
MD5StateAppend(&obj->md5, hd, hd_sz);
if( g_dump ) {
fwrite(hd, hd_sz, 1, stderr);
}
}
}
}
obj->file_size += written;
blk += written;
inode->id_qty++;
MD5StateAppend(&obj->md5, buffer, written);
if( g_dump ) {
fwrite(buffer, written, 1, stderr);
}
}
rc = rc ? rc : Quitting();
if( rc != 0 ) {
spotid_t spot = 0;
SFFReaderCurrentSpot(reader, &spot);
PLOGERR(klogErr, (klogErr, rc, "spot $(s)", PLOG_U32(s), spot));
}
}
SFFReaderWhack(reader);
return rc;
}示例4: Fastq_Idx
static
rc_t Fastq_Idx(const SRATable* sratbl, SIndexObj* obj, char* buffer, const size_t buffer_sz)
{
rc_t rc = 0;
const FastqReader* reader = NULL;
uint8_t colorSpace = false;
char* colorSpaceKey = "\0";
uint8_t origFormat = false;
uint8_t printLabel = true;
uint8_t printReadId = true;
uint8_t clipQuality = true;
uint32_t minReadLen = 0;
uint16_t qualityOffset = 0;
{{
const SRAColumn* c = NULL;
const uint8_t *platform = SRA_PLATFORM_UNDEFINED;
bitsz_t o, z;
if( (rc = SRATableOpenColumnRead(sratbl, &c, "PLATFORM", sra_platform_id_t)) != 0 ) {
return rc;
}
if( (rc = SRAColumnRead(c, 1, (const void **)&platform, &o, &z)) != 0 ) {
return rc;
}
if( *platform == SRA_PLATFORM_ABSOLID ) {
colorSpace = true;
}
SRAColumnRelease(c);
}}
if( (rc = FastqReaderMake(&reader, sratbl, g_accession,
colorSpace, origFormat, false, printLabel, printReadId,
!clipQuality, minReadLen, qualityOffset, colorSpaceKey[0],
obj->minSpotId, obj->maxSpotId)) != 0 ) {
return rc;
} else {
KMDataNode* opt = NULL, *nd = NULL;
if( (rc = KMDataNodeOpenNodeUpdate(obj->meta, &opt, "Format/Options")) != 0 ) {
return rc;
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "colorSpace")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &colorSpace);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "colorSpaceKey")) == 0 ) {
rc = KMDataNodeWrite(nd, colorSpaceKey, 1);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "origFormat")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &origFormat);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "printLabel")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &printLabel);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "printReadId")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &printReadId);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "clipQuality")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &clipQuality);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "minReadLen")) == 0 ) {
rc = KMDataNodeWriteB32(nd, &minReadLen);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "qualityOffset")) == 0 ) {
rc = KMDataNodeWriteB16(nd, &qualityOffset);
KMDataNodeRelease(nd);
}
KMDataNodeRelease(opt);
}
if( rc == 0 ) {
size_t written = 0;
uint32_t blk = 0;
SIndexNode* inode = NULL;
while( rc == 0 ) {
rc = FastqReader_GetNextSpotSplitData(reader, buffer, buffer_sz, &written);
if( blk >= g_file_block_sz || (GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted) ) {
inode->key_size = blk;
SLListPushTail(&obj->li, &inode->n);
DEBUG_MSG(5, ("Fastq index closed spots %lu, offset %lu, block size %lu\n",
inode->id_qty, inode->key, inode->key_size));
inode = NULL;
if( blk > obj->buffer_sz ) {
obj->buffer_sz = blk;
}
blk = 0;
}
if( GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted ) {
rc = 0;
break;
}
//.........这里部分代码省略.........
示例5: FastqReaderFileGetRecord
rc_t FastqReaderFileGetRecord ( const FastqReaderFile *f, const Record** result )
{
rc_t rc;
FastqReaderFile* self = (FastqReaderFile*) f;
if (self->pb.fatalError)
return 0;
self->pb.record = (FastqRecord*)malloc(sizeof(FastqRecord));
if (self->pb.record == NULL)
{
rc = RC ( RC_MODULE, rcData, rcAllocating, rcMemory, rcExhausted );
return 0;
}
rc = FastqRecordInit(self->pb.record);
if (rc != 0)
return rc;
FASTQ_ParseBlockInit( & self->pb );
if ( FASTQ_parse( & self->pb ) == 0 && self->pb.record->rej == 0 )
{ /* normal end of input */
RecordRelease((const Record*)self->pb.record);
*result = 0;
return 0;
}
/*TODO: remove? compensate for an artificially inserted trailing \n */
if ( self->eolInserted )
{
-- self->pb.length;
self->eolInserted = false;
}
if (self->pb.record->rej != 0) /* had error(s) */
{ /* save the complete raw source in the Rejected object */
StringInit(& self->pb.record->rej->source, string_dup(self->recordStart, self->pb.length), self->pb.length, (uint32_t)self->pb.length);
self->pb.record->rej->fatal = self->pb.fatalError;
}
if (rc == 0 && self->reader != 0)
{
/* advance the record start pointer beyond the last token */
size_t length;
rc = KLoaderFile_Read( self->reader, self->pb.length, 0, (const void**)& self->recordStart, & length);
if (rc != 0)
LogErr(klogErr, rc, "FastqReaderFileGetRecord failed");
self->curPos -= self->pb.length;
}
StringInit( & self->pb.record->seq.spotname, (const char*)self->pb.record->source.base + self->pb.spotNameOffset, self->pb.spotNameLength, (uint32_t)self->pb.spotNameLength);
StringInit( & self->pb.record->seq.spotgroup, (const char*)self->pb.record->source.base + self->pb.spotGroupOffset, self->pb.spotGroupLength, (uint32_t)self->pb.spotGroupLength);
StringInit( & self->pb.record->seq.read, (const char*)self->pb.record->source.base + self->pb.readOffset, self->pb.readLength, (uint32_t)self->pb.readLength);
StringInit( & self->pb.record->seq.quality, (const char*)self->pb.record->source.base + self->pb.qualityOffset, self->pb.qualityLength, (uint32_t)self->pb.qualityLength);
self->pb.record->seq.qualityFormat = self->pb.qualityFormat;
self->pb.record->seq.qualityAsciiOffset = self->pb.qualityAsciiOffset;
if (self->pb.record->seq.readnumber == 0)
self->pb.record->seq.readnumber = self->pb.defaultReadNumber;
*result = (const Record*) self->pb.record;
return rc;
}示例6: RC
* neither.
*
* This list should probably be more configurable, and more than
* likely on a per-realm basis, so locally-defined services can be
* added, or not.
*/
static const struct krb_convert sconv_list[] = {
/* Realm conversion, Change service name */
#define RC(V5NAME,V4NAME) { V5NAME, V4NAME, DO_REALM_CONVERSION, sizeof(V5NAME)-1 }
/* Realm conversion */
#define R(NAME) { NAME, NAME, DO_REALM_CONVERSION, sizeof(NAME)-1 }
/* No Realm conversion */
#define NR(NAME) { NAME, NAME, 0, sizeof(NAME)-1 }
NR("kadmin"),
RC("rcmd", "host"),
R("discuss"),
R("rvdsrv"),
R("sample"),
R("olc"),
R("pop"),
R("sis"),
R("rfs"),
R("imap"),
R("ftp"),
R("ecat"),
R("daemon"),
R("gnats"),
R("moira"),
R("prms"),
R("mandarin"),示例7: align_info
static rc_t align_info(const Params* prm) {
rc_t rc = 0;
const VDatabase* db = NULL;
const VDBManager* mgr = NULL;
const KDBManager *kmgr = NULL;
VSchema* schema = NULL;
bool is_db = false;
if (prm == NULL)
{ return RC(rcExe, rcQuery, rcExecuting, rcParam, rcNull); }
if (rc == 0) {
rc = VDBManagerMakeRead(&mgr, NULL);
DISP_RC(rc, "while calling VDBManagerMakeRead");
}
if (rc == 0) {
rc = VDBManagerOpenKDBManagerRead(mgr, &kmgr);
DISP_RC(rc, "while calling VDBManagerOpenKDBManagerRead");
}
if (rc == 0) {
rc = VDBManagerMakeSRASchema(mgr, &schema);
DISP_RC(rc, "while calling VDBManagerMakeSRASchema");
}
if (rc == 0) {
rc = VDBManagerOpenDBRead(mgr, &db, schema, prm->dbPath);
if (rc == 0) {
is_db = true;
}
else if (rc == SILENT_RC(rcDB, rcMgr, rcOpening, rcDatabase, rcIncorrect)) {
PLOGMSG(klogWarn, (klogWarn,
"'$(path)' is not a database", "path=%s", prm->dbPath));
rc = 0;
}
else {
PLOGERR(klogErr,
(klogErr, rc, "$(path)", "path=%s", prm->dbPath));
}
}
if (is_db) {
if (rc == 0) {
if (prm->paramRef) {
const VDBDependencies* dep = NULL;
uint32_t count = 0;
int i = 0;
if (prm->paramHeaders) {
OUTMSG(("Alignments:\n"));
}
rc = VDatabaseListDependencies(db, &dep, false);
DISP_RC2(rc, prm->dbPath,
"while calling VDatabaseListDependencies");
if (rc == 0) {
rc = VDBDependenciesCount(dep, &count);
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesCount");
}
for (i = 0; i < count && rc == 0; ++i) {
bool circular = false;
const char* name = NULL;
const char* path = NULL;
const char* remote = NULL;
bool local = false;
const char* seqId = NULL;
rc = VDBDependenciesCircular(dep, &circular, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesCircular");
break;
}
rc = VDBDependenciesName(dep, &name, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesName");
break;
}
rc = VDBDependenciesPath(dep, &path, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesPath");
break;
}
rc = VDBDependenciesLocal(dep, &local, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesLocal");
break;
}
rc = VDBDependenciesSeqId(dep, &seqId, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesSeqId");
break;
}
rc = VDBDependenciesPathRemote(dep, &remote, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
//.........这里部分代码省略.........
示例8: KMain
rc_t CC KMain(int argc, char* argv[]) {
rc_t rc = 0;
Args* args = NULL;
Params prm;
memset(&prm, 0, sizeof prm);
do {
uint32_t pcount = 0;
rc = ArgsMakeAndHandle(&args, argc, argv, 1,
Options, sizeof Options / sizeof (OptDef));
if (rc) {
LOGERR(klogErr, rc, "While calling ArgsMakeAndHandle");
break;
}
rc = ArgsParamCount(args, &pcount);
if (rc) {
LOGERR(klogErr, rc, "While calling ArgsParamCount");
break;
}
if (pcount < 1) {
MiniUsage(args);
DESTRUCT(Args, args);
exit(1);
break;
}
if (pcount > 1) {
rc = RC(rcExe, rcArgv, rcParsing, rcParam, rcAmbiguous);
LOGERR(klogErr, rc, "Too many database parameters");
break;
}
rc = ArgsParamValue(args, 0, &prm.dbPath);
if (rc) {
LOGERR(klogErr, rc, "Failure retrieving database name");
break;
}
rc = ArgsOptionCount (args, OPTION_ALL, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_ALL "' argument");
break;
}
if (pcount)
{ prm.paramBamHeader = prm.paramQuality = prm.paramRef = true; }
rc = ArgsOptionCount (args, OPTION_BAM, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_BAM "' argument");
break;
}
if (pcount)
{ prm.paramBamHeader = true; }
rc = ArgsOptionCount (args, OPTION_QUA, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_QUA "' argument");
break;
}
if (pcount)
{ prm.paramQuality = true; }
rc = ArgsOptionCount (args, OPTION_REF, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_REF "' argument");
break;
}
if (pcount)
{ prm.paramRef = true; }
if (!prm.paramBamHeader && !prm.paramQuality && !prm.paramRef)
{ prm.paramRef = true; }
rc = ArgsOptionCount (args, OPTION_HEA, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_HEA "' argument");
break;
}
if (pcount) {
prm.paramHeaders = true;
}
} while (false);
if (rc == 0)
{ rc = align_info(&prm); }
DESTRUCT(Args, args);
return rc;
}示例9: SFFGzip_Idx
static
rc_t SFFGzip_Idx(const SRATable* sratbl, SIndexObj* obj, char* buffer, const size_t buffer_sz)
{
rc_t rc = 0;
uint16_t zlib_ver = ZLIB_VERNUM;
const SFFReader* reader = NULL;
if( (rc = SFFReaderMake(&reader, sratbl, g_accession, obj->minSpotId, obj->maxSpotId)) != 0 ) {
return rc;
} else {
size_t written = 0;
uint32_t blk = 0, spots_per_block = 0, proj_id_qty = 0;
SIndexNode* inode = NULL;
size_t z_blk = 0;
size_t spots_buf_sz = g_file_block_sz * 100;
size_t zbuf_sz = spots_buf_sz + 100;
char* zbuf = malloc(zbuf_sz);
char* spots_buf = malloc(spots_buf_sz);
bool eof = false;
if( zbuf == NULL || spots_buf == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
}
while( rc == 0 ) {
if( (rc = SFFReader_GetNextSpotData(reader, buffer, buffer_sz, &written)) == 0 ) {
if( inode == NULL ) {
spotid_t spotid = 0;
if( (rc = SFFReaderCurrentSpot(reader, &spotid)) != 0 ) {
break;
}
inode = malloc(sizeof(SIndexNode));
if( inode == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
break;
}
inode->key = obj->file_size;
inode->key_size = 0;
inode->id = spotid;
inode->id_qty = 0;
DEBUG_MSG(5, ("%s open key: spot %ld, offset %lu\n", obj->index, inode->id, inode->key));
if( spotid == 1 ) {
char hd[10240];
size_t hd_sz = 0;
if( (rc = SFFReaderHeader(reader, 0, hd, sizeof(hd), &hd_sz)) == 0 ) {
if( hd_sz + written > spots_buf_sz ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcInsufficient);
break;
}
memmove(&spots_buf[blk], hd, hd_sz);
blk += hd_sz;
if( g_dump ) {
fwrite(hd, hd_sz, 1, stderr);
}
}
}
}
if( blk + written > spots_buf_sz ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcInsufficient);
break;
}
inode->id_qty++;
memmove(&spots_buf[blk], buffer, written);
blk += written;
if( g_dump ) {
fwrite(buffer, written, 1, stderr);
}
}
if( (eof = (GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted)) ) {
rc = 0;
if( inode == NULL ) {
break;
}
}
if( rc == 0 && (eof ||
(proj_id_qty == 0 && inode->id_qty > (spots_per_block * 0.95)) ||
(proj_id_qty > 0 && inode->id_qty >= proj_id_qty) ) ) {
rc = ZLib_DeflateBlock(spots_buf, blk, zbuf, zbuf_sz, &z_blk);
if( z_blk < g_file_block_sz ) {
/* project needed id_qty */
proj_id_qty = g_file_block_sz * inode->id_qty / z_blk * 1.05;
DEBUG_MSG(5, ("%s: project id qty %lu\n", obj->index, proj_id_qty));
} else {
DEBUG_MSG(10, ("%s: no projection %lu > %lu\n", obj->index, z_blk, g_file_block_sz));
}
}
if( rc == 0 && (eof || z_blk >= g_file_block_sz) ) {
obj->file_size += z_blk;
MD5StateAppend(&obj->md5, zbuf, z_blk);
inode->key_size = z_blk;
SLListPushTail(&obj->li, &inode->n);
DEBUG_MSG(5, ("%s close key: spots %lu, size %lu, ratio %hu%%, raw %lu\n",
obj->index, inode->id_qty, inode->key_size, (uint16_t)(((float)(blk - z_blk)/blk)*100), blk));
spots_per_block = inode->id_qty;
inode = NULL;
if( blk > obj->buffer_sz ) {
obj->buffer_sz = blk;
}
blk = 0;
//.........这里部分代码省略.........
示例10: KNSManagerInitDNSEndpoint
/* InitDNSEndpoint
* initialize the endpoint with a DNS name and a port number
*
* "ep" [ OUT ] - address of endpoint block to be intialized
*
* "dns" [ IN ] - textual DNS address.
*
* "port" [ IN, DEFAULT 0 ] - binary port number in native integer byte order.
* if the special port number 0 is given, it represents any available port.
*/
LIB_EXPORT
rc_t CC KNSManagerInitDNSEndpoint ( struct KNSManager const *self,
KEndPoint *ep, struct String const *dns, uint16_t port )
{
rc_t rc = 0;
if ( ep == NULL )
rc = RC (rcNS, rcNoTarg, rcInitializing, rcParam, rcNull );
else
{
if ( self == NULL )
rc = RC ( rcNS, rcNoTarg, rcInitializing, rcSelf, rcNull );
else if ( dns == NULL )
rc = RC ( rcNS, rcNoTarg, rcInitializing, rcParam, rcNull );
else if ( dns -> size == 0 )
rc = RC ( rcNS, rcNoTarg, rcInitializing, rcSelf, rcInsufficient );
else
{
KDataBuffer b;
char buffer [ 4096 ], * hostname = buffer;
size_t buff_size = sizeof buffer;
if ( dns -> size >= sizeof buffer )
{
rc = KDataBufferMakeBytes ( & b, dns -> size + 1 );
if ( rc == 0 )
{
hostname = b . base;
buff_size = ( size_t ) b . elem_count;
}
}
if ( rc == 0 )
{
size_t size;
rc = string_printf ( hostname, buff_size, & size, "%S", dns );
assert ( rc == 0 );
assert ( size < buff_size );
assert ( hostname [ size ] == 0 );
if ( rc == 0 )
{
int lerrno;
struct hostent *remote = gethostbyname ( hostname );
if ( remote != NULL )
{
ep -> type = epIPV4;
memcpy ( & ep -> u . ipv4 . addr, remote -> h_addr_list [ 0 ], sizeof ep -> u . ipv4 . addr );
ep -> u . ipv4 . addr = htonl ( ep -> u . ipv4 . addr );
ep -> u . ipv4 . port = ( uint16_t ) port;
}
else switch ( lerrno = WSAGetLastError () )
{
case WSANOTINITIALISED: /* Must have WSAStartup call */
rc = RC ( rcNS, rcNoTarg, rcInitializing, rcEnvironment, rcUndefined );
break;
case WSAENETDOWN:/* network subsystem failed */
rc = RC ( rcNS, rcNoTarg, rcInitializing, rcNoObj, rcFailed );
break;
case WSAHOST_NOT_FOUND: /* Answer host not found */
rc = RC ( rcNS, rcNoTarg, rcValidating, rcConnection, rcNotFound );
break;
case WSATRY_AGAIN: /* host not found or server failure */
rc = RC ( rcNS, rcNoTarg, rcValidating, rcConnection, rcBusy );
break;
case WSANO_RECOVERY: /* non-recoverable error */
rc = RC ( rcNS, rcNoTarg, rcValidating, rcConnection, rcError );
break;
case WSANO_DATA: /* name is valid but no data */
rc = RC ( rcNS, rcNoTarg, rcValidating, rcConnection, rcEmpty );
break;
case WSAEINPROGRESS: /* call is in progress */
rc = RC ( rcNS, rcNoTarg, rcReading, rcId, rcUndefined );
break;
case WSAEFAULT: /* name paremeter is not valid part of addr space */
rc = RC ( rcNS, rcNoTarg, rcReading, rcMemory, rcOutofrange );
break;
case WSAEINTR: /* socket call was calanceled */
rc = RC ( rcNS, rcNoTarg, rcReading, rcConnection, rcCanceled );
break;
default:
rc = RC ( rcNS, rcNoTarg, rcReading, rcNoObj, rcError );
}
}
}
if ( hostname != buffer )
KDataBufferWhack ( & b );
}
//.........这里部分代码省略.........
示例11: FastqGzip_Idx
static
rc_t FastqGzip_Idx(const SRATable* sratbl, SIndexObj* obj, char* buffer, const size_t buffer_sz)
{
rc_t rc = 0;
const FastqReader* reader = NULL;
uint16_t zlib_ver = ZLIB_VERNUM;
uint8_t colorSpace = false;
char* colorSpaceKey = "\0";
uint8_t origFormat = false;
uint8_t printLabel = true;
uint8_t printReadId = true;
uint8_t clipQuality = true;
uint32_t minReadLen = 0;
uint16_t qualityOffset = 0;
{{
const SRAColumn* c = NULL;
const uint8_t *platform = SRA_PLATFORM_UNDEFINED;
bitsz_t o, z;
if( (rc = SRATableOpenColumnRead(sratbl, &c, "PLATFORM", sra_platform_id_t)) != 0 ) {
return rc;
}
if( (rc = SRAColumnRead(c, 1, (const void **)&platform, &o, &z)) != 0 ) {
return rc;
}
if( *platform == SRA_PLATFORM_ABSOLID ) {
colorSpace = true;
}
SRAColumnRelease(c);
}}
if( (rc = FastqReaderMake(&reader, sratbl, g_accession,
colorSpace, origFormat, false, printLabel, printReadId,
!clipQuality, minReadLen, qualityOffset, colorSpaceKey[0],
obj->minSpotId, obj->maxSpotId)) != 0 ) {
return rc;
} else {
size_t written = 0;
uint32_t blk = 0, spots_per_block = 0, proj_id_qty = 0;
SIndexNode* inode = NULL;
size_t z_blk = 0;
size_t spots_buf_sz = g_file_block_sz * 100;
size_t zbuf_sz = spots_buf_sz + 100;
char* zbuf = malloc(zbuf_sz);
char* spots_buf = malloc(spots_buf_sz);
bool eof = false;
if( zbuf == NULL || spots_buf == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
}
while( rc == 0 ) {
if( (rc = FastqReader_GetNextSpotSplitData(reader, buffer, buffer_sz, &written)) == 0 ) {
if( inode == NULL ) {
spotid_t spotid = 0;
if( (rc = FastqReaderCurrentSpot(reader, &spotid)) != 0 ) {
break;
}
inode = malloc(sizeof(SIndexNode));
if( inode == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
break;
}
inode->key = obj->file_size;
inode->key_size = 0;
inode->id = spotid;
inode->id_qty = 0;
DEBUG_MSG(5, ("%s open key: spot %ld, offset %lu\n", obj->index, inode->id, inode->key));
}
if( blk + written > spots_buf_sz ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcInsufficient);
break;
}
inode->id_qty++;
memmove(&spots_buf[blk], buffer, written);
blk += written;
if( g_dump ) {
fwrite(buffer, written, 1, stderr);
}
}
if( (eof = (GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted)) ) {
rc = 0;
if( inode == NULL ) {
break;
}
}
if( rc == 0 && (eof ||
(proj_id_qty == 0 && inode->id_qty > (spots_per_block * 0.95)) ||
(proj_id_qty > 0 && inode->id_qty >= proj_id_qty) ) ) {
rc = ZLib_DeflateBlock(spots_buf, blk, zbuf, zbuf_sz, &z_blk);
if( z_blk < g_file_block_sz ) {
/* project needed id_qty */
proj_id_qty = g_file_block_sz * inode->id_qty / z_blk * 1.05;
DEBUG_MSG(5, ("%s: project id qty %u\n", obj->index, proj_id_qty));
} else {
DEBUG_MSG(10, ("%s: no projection %u > %u\n", obj->index, z_blk, g_file_block_sz));
}
}
if( rc == 0 && (eof || z_blk >= g_file_block_sz) ) {
//.........这里部分代码省略.........
示例12: KMain
rc_t KMain(int argc, char *argv[])
{
rc_t rc = 0;
Args* args = NULL;
const char* errmsg = NULL, *table_dir = NULL;
char accn[1024];
if( (rc = ArgsMakeAndHandle(&args, argc, argv, 1, MainArgs, MainArgsQty)) == 0 ) {
const char* blksz = NULL;
uint32_t count, dump = 0, gzip = 0;
if( (rc = ArgsParamCount(args, &count)) != 0 || count != 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, count > 1 ? rcExcessive : rcInsufficient);
errmsg = "table";
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_BlockSize].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_BlockSize].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_BlockSize].name, 0, (const void **)&blksz)) != 0 ) {
errmsg = MainArgs[eopt_BlockSize].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_Accession].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_Accession].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_Accession].name, 0, (const void **)&g_accession)) != 0 ) {
errmsg = MainArgs[eopt_Accession].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_DumpIndex].name, &dump)) != 0 ) {
errmsg = MainArgs[eopt_DumpIndex].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_noGzip].name, &gzip)) != 0 ) {
errmsg = MainArgs[eopt_noGzip].name;
}
while( rc == 0 ) {
long val = 0;
char* end = NULL;
if( blksz != NULL ) {
errno = 0;
val = strtol(blksz, &end, 10);
if( errno != 0 || blksz == end || *end != '\0' || val <= 0 ) {
rc = RC(rcExe, rcArgv, rcReading, rcParam, rcInvalid);
errmsg = MainArgs[eopt_BlockSize].name;
break;
} else if( val <= 128 || val > (1024 * 1024 * 1024) ) {
rc = RC(rcExe, rcArgv, rcValidating, rcParam, rcEmpty);
errmsg = "block size invalid";
break;
}
g_file_block_sz = val;
}
if( (rc = ArgsParamValue(args, 0, (const void **)&table_dir)) != 0 ) {
errmsg = "table";
break;
}
if( g_accession == NULL ) {
const char* p = strchr(table_dir, '/');
size_t l = 0;
g_accession = accn;
if( p == NULL ) {
p = strchr(table_dir, '\\');
}
strncpy(accn, p == NULL ? table_dir : p + 1, sizeof(accn) - 1);
if( accn[0] == '\0' ) {
rc = RC(rcExe, rcArgv, rcValidating, rcParam, rcEmpty);
errmsg = "accession";
}
l = strlen(accn);
if( accn[l - 1] == '/' || accn[l - 1] == '\\') {
accn[--l] = '\0';
}
if( strncmp(&accn[l - 9], ".lite.sra", 9) == 0 ) {
accn[l - 9] = '\0';
} else if( strncmp(&accn[l - 4], ".sra", 4) == 0 ) {
accn[l - 4] = '\0';
}
}
g_dump = dump > 0;
g_ungzip = gzip > 0;
break;
}
}
if( rc == 0 ) {
SRAMgr* smgr = NULL;
KDBManager* kmgr = NULL;
DEBUG_MSG(5, ("table %s, accession %s\n", table_dir, g_accession));
if( (rc = SRAMgrMakeUpdate(&smgr, NULL)) == 0 ) {
if( (rc = KDBManagerMakeUpdate(&kmgr, NULL)) == 0 ) {
bool relock = true;
if( (rc = KDBManagerUnlock(kmgr, table_dir)) != 0 ) {
relock = false;
rc = GetRCState(rc) == rcUnlocked ? 0 : rc;
} else {
PLOGMSG(klogInfo, (klogInfo, "Table $(p) locked, unlocking", PLOG_S(p), table_dir));
}
if( rc == 0 ) {
KTable* ktbl = NULL;
if( (rc = KDBManagerOpenTableUpdate(kmgr, &ktbl, table_dir)) == 0 ) {
//.........这里部分代码省略.........
示例13: extract_statistic_from_row
rc_t extract_statistic_from_row(statistic *self,
row_input const *data)
{
rc_t rc = 0;
spotgrp *sg;
char const *spotgrp_base;
uint32_t spotgrp_len;
unsigned i;
uint8_t lb = 4;
unsigned hpr = 0;
unsigned gcc = 0;
if (data == NULL) {
return RC(rcXF, rcFunction, rcExecuting, rcParam, rcNull);
}
if (self == NULL) {
return RC(rcXF, rcFunction, rcExecuting, rcSelf, rcNull);
}
rc = validate_row_data(self, data);
if (rc)
return rc;
spotgrp_base = data->spotgroup;
spotgrp_len = data->spotgroup_len;
if (spotgrp_base == NULL || spotgrp_len == 0) {
spotgrp_base = "";
spotgrp_len = 0;
}
sg = find_spotgroup( self, spotgrp_base, spotgrp_len );
if ( sg == NULL )
{
sg = make_spotgrp( spotgrp_base, spotgrp_len );
if ( sg == NULL )
{
return RC( rcXF, rcFunction, rcExecuting, rcMemory, rcExhausted );
}
else
{
rc = BSTreeInsert ( &self->spotgroups, (BSTNode *)sg, spotgroup_sort );
if (rc)
return rc;
}
}
for (i = 0; i < data->read_len && rc == 0; ++i) {
unsigned const base = data->read[i];
unsigned dimer;
if (base > 3) {
dimer = 16;
hpr = 0;
}
else {
dimer = (lb > 3) ? 16 : ((lb << 2) | base);
if (lb == base)
++hpr;
else
hpr = 0;
}
if (i > 0)
rc = spotgroup_enter_values(sg, data->quality[i], dimer, gcc, hpr, data->base_pos_offset + i, CASE_MATCH);
if (base == 1 || base == 2)
++gcc;
if (i >= self->gc_window) {
unsigned const out = data->read[i - self->gc_window];
if (out == 1 || out == 2)
--gcc;
}
lb = base;
}
return rc;
}示例14: qual_stats
static rc_t qual_stats(const Params* prm, const VDatabase* db) {
rc_t rc = 0;
const char tblName[] = "SEQUENCE";
const VTable* tbl = NULL;
const KMetadata* meta = NULL;
const KMDataNode* node = NULL;
assert(prm && db);
if (rc == 0) {
rc = VDatabaseOpenTableRead(db, &tbl, tblName);
DISP_RC2(rc, tblName, "while calling VDatabaseOpenTableRead");
}
if (rc == 0) {
rc = VTableOpenMetadataRead(tbl, &meta);
DISP_RC2(rc, tblName, "while calling VTableOpenMetadataRead");
}
if (rc == 0) {
bool found = false;
const char path[] = "STATS/QUALITY";
rc = KMetadataOpenNodeRead(meta, &node, path);
if (rc == 0)
{ found = true; }
else if (GetRCState(rc) == rcNotFound)
{ rc = 0; }
DISP_RC2(rc, path, "while calling KMetadataOpenNodeRead");
if (found) {
uint32_t i = 0;
int nbr = 0;
uint32_t count = 0;
KNamelist* names = NULL;
int* quals = NULL;
if (rc == 0) {
rc = KMDataNodeListChild(node, &names);
DISP_RC2(rc, path, "while calling KMDataNodeListChild");
}
if (rc == 0) {
rc = KNamelistCount(names, &count);
DISP_RC2(rc, path, "while calling KNamelistCount");
if (rc == 0 && count > 0) {
quals = calloc(count, sizeof *quals);
if (quals == NULL) {
rc = RC(rcExe,
rcStorage, rcAllocating, rcMemory, rcExhausted);
}
}
}
for (i = 0; i < count && rc == 0; ++i) {
/* uint64_t u = 0;
const KMDataNode* n = NULL; */
const char* nodeName = NULL;
const char* name = NULL;
rc = KNamelistGet(names, i, &nodeName);
DISP_RC2(rc, path, "while calling KNamelistGet");
if (rc)
{ break; }
name = nodeName;
/* rc = KMDataNodeOpenNodeRead(node, &n, name);
DISP_RC(rc, name);
if (rc == 0) {
rc = KMDataNodeReadAsU64(n, &u);
DISP_RC(rc, name);
} */
if (rc == 0) {
char* c = strchr(name, '_');
if (c != NULL && *(c + 1) != '\0') {
name = c + 1;
if (sscanf(name, "%d", &quals[i]) != 1) {
rc = RC(rcExe,
rcNode, rcParsing, rcName, rcUnexpected);
PLOGERR(klogInt,
(klogInt, rc, "$(name)", "name=%s", nodeName));
}
}
/* OUTMSG(("QUALITY %s %lu\n", name, u)); */
}
/* DESTRUCT(KMDataNode, n); */
}
if (rc == 0 && count > 0)
{ ksort(quals, count, sizeof *quals, sort_callback, NULL); }
if (rc == 0) {
if (prm->paramHeaders) {
OUTMSG(("Quality statistics - rows per value\n"));
OUTMSG(("Quality values:"));
for (i = 0; i <= 40; ++i) {
OUTMSG(("\t%d", i));
}
OUTMSG(("\n"));
}
OUTMSG(("%s", prm->dbPath));
}
for (i = 0, nbr = 0; i < count && rc == 0; ++i, ++nbr) {
uint64_t u = 0;
char name[64];
const KMDataNode* n = NULL;
sprintf(name, "PHRED_%d", quals[i]);
rc = KMDataNodeOpenNodeRead(node, &n, name);
DISP_RC(rc, name);
if (rc == 0) {
rc = KMDataNodeReadAsU64(n, &u);
//.........这里部分代码省略.........
示例15: kqsh_alter_cursor_add_column
/* alter cursor
* 'alter <cursor> add column [ ( <typedecl> ) ] NAME;'
*
* all data after the 'column' keyword are gathered into
* ( typedecl, name ) pairs. we are going to allow comma
* separation, but otherwise just gather everything up to
* the semi-colon.
*/
static
rc_t kqsh_alter_cursor_add_column ( KSymTable *tbl, KTokenSource *src, KToken *t, KSymbol *cursor )
{
rc_t rc;
do
{
size_t i;
uint32_t idx;
char coldecl [ 256 ];
for ( i = 0; i < sizeof coldecl - 1; )
{
/* end of column */
if ( t -> id == eSemiColon || t -> id == eComma )
break;
/* accumulate */
i += string_copy ( & coldecl [ i ],
sizeof coldecl - i, t -> str . addr, t -> str . size );
next_token ( tbl, src, t );
}
/* the name needs to fit in our buffer */
if ( i == sizeof coldecl - 1 )
{
rc = RC ( rcExe, rcCursor, rcUpdating, rcName, rcExcessive );
if ( interactive )
{
kqsh_printf ( "this is really hard to believe, but you managed to request\n"
"a column with a %u byte expression. please stop trying to abuse me.\n",
( unsigned int ) i );
}
else
{
LOGERR ( klogErr, rc, "failed to add column to cursor" );
}
return rc;
}
/* perform the task */
rc = _VCursorAddColumn ( cursor -> u . obj, & idx, coldecl );
if ( rc != 0 )
{
PLOGERR ( klogErr, (klogErr, rc, "cannot add column '$(expr)' to cursor '$(curs)'",
"expr=%s,curs=%.*s"
, coldecl
, ( int ) cursor -> name . size, cursor -> name . addr));
}
else if ( interactive )
{
kqsh_printf ( "added column '%s' ( idx %u ) to cursor '%N' ( %p )\n"
, coldecl
, idx
, cursor
, cursor -> u . obj
);
}
}
while ( t -> id == eComma );
if ( t -> id != eSemiColon )
return expected ( t, klogErr, ";" );
return 0;
}