/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/ |
H A D | ReadsSparkSinkUnitTest.java | 130 final java.nio.file.Path subpath = defaultPartsDir.resolve("subpath"); in testSpecifyPartsDir() local 135 Files.createFile(subpath); in testSpecifyPartsDir()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/align/nw/ |
H A D | mm_aligner.hpp | 96 list<ETranscriptSymbol>& subpath); 114 list<ETranscriptSymbol>& subpath) const;
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/nw/ |
H A D | mm_aligner.cpp | 371 list<ETranscriptSymbol>& subpath ) const in x_ExtendSubpath() 373 subpath.clear(); in x_ExtendSubpath() 379 subpath.push_back(eTS_Match); in x_ExtendSubpath() 384 subpath.push_back(eTS_Insert); in x_ExtendSubpath() 394 subpath.push_back(eTS_Delete); in x_ExtendSubpath() 408 subpath.push_front(eTS_Match); in x_ExtendSubpath() 413 subpath.push_front(eTS_Insert); in x_ExtendSubpath() 423 subpath.push_front(eTS_Delete); in x_ExtendSubpath() 905 subpath.clear(); in x_RunTerm() 912 subpath.push_front(eTS_Match); in x_RunTerm() [all …]
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/dports/biology/ncbi-toolkit/ncbi/link/macmet/ |
H A D | setrsrc.c | 306 static void RecurseDir (char * directory, char * subpath) in RecurseDir() argument 315 MyFileBuildPath (path, subpath, NULL); in RecurseDir()
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/kdb/ |
H A D | kdb-priv.h | 103 char *subpath, size_t subpath_max, const char *ns, 109 char *subpath, size_t subpath_max, const char *ns,
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H A D | kdb.c | 853 char *subpath, size_t subpath_max, const char *ns, in KDBVMakeSubPath() argument 860 subpath += ns_size + 1; in KDBVMakeSubPath() 868 subpath, subpath_max, path, args ); in KDBVMakeSubPath() 871 int sz = vsnprintf ( subpath, subpath_max, path, args ); in KDBVMakeSubPath() 885 assert ( subpath [ 0 ] != 0 ); in KDBVMakeSubPath() 886 if ( subpath [ 0 ] == '.' || subpath [ 1 ] == '/' ) in KDBVMakeSubPath() 897 subpath -= ns_size + 1; in KDBVMakeSubPath() 898 memmove ( subpath, ns, ns_size ); in KDBVMakeSubPath() 899 subpath [ ns_size ] = '/'; in KDBVMakeSubPath() 908 char *subpath, size_t subpath_max, const char *ns, in KDBMakeSubPath() argument [all …]
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H A D | wkdb-priv.h | 130 char *subpath, size_t subpath_max, const char *ns, 136 char *subpath, size_t subpath_max, const char *ns,
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H A D | wkdb.c | 1038 char *subpath, size_t subpath_max, const char *ns, in KDBVMakeSubPath() argument 1045 subpath += ns_size + 1; in KDBVMakeSubPath() 1053 subpath, subpath_max, path, args ); in KDBVMakeSubPath() 1056 int sz = vsnprintf ( subpath, subpath_max, path, args ); in KDBVMakeSubPath() 1070 assert ( subpath [ 0 ] != 0 ); in KDBVMakeSubPath() 1071 if ( subpath [ 0 ] == '.' || subpath [ 1 ] == '/' ) in KDBVMakeSubPath() 1082 subpath -= ns_size + 1; in KDBVMakeSubPath() 1083 memmove ( subpath, ns, ns_size ); in KDBVMakeSubPath() 1084 subpath [ ns_size ] = '/'; in KDBVMakeSubPath() 1093 char *subpath, size_t subpath_max, const char *ns, in KDBMakeSubPath() argument [all …]
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/dports/biology/p5-Bio-Glite/Bio-Glite-0.10/inc/Module/ |
H A D | Install.pm | 239 my $subpath = $1; 240 return if lc($subpath) eq lc($self->{dispatch}); 242 $file = "$self->{path}/$subpath.pm"; 243 my $pkg = "$self->{name}::$subpath"; 249 if ( $subpath eq lc($subpath) || $subpath eq uc($subpath) ) { 250 open PKGFILE, "<$subpath.pm" or die "find_extensions: Can't open $subpath.pm: $!";
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/dports/biology/p5-Bio-MAGETAB/Bio-MAGETAB-1.31/inc/Module/ |
H A D | Install.pm | 328 my $subpath = $1; 329 return if lc($subpath) eq lc($self->{dispatch}); 331 $file = "$self->{path}/$subpath.pm"; 332 my $pkg = "$self->{name}::$subpath"; 338 if ( $subpath eq lc($subpath) || $subpath eq uc($subpath) ) { 339 my $content = Module::Install::_read($subpath . '.pm');
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/kdb/ |
H A D | kdb-priv.h | 103 char *subpath, size_t subpath_max, const char *ns, 109 char *subpath, size_t subpath_max, const char *ns,
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H A D | kdb.c | 853 char *subpath, size_t subpath_max, const char *ns, in KDBVMakeSubPath() argument 860 subpath += ns_size + 1; in KDBVMakeSubPath() 868 subpath, subpath_max, path, args ); in KDBVMakeSubPath() 871 int sz = vsnprintf ( subpath, subpath_max, path, args ); in KDBVMakeSubPath() 885 assert ( subpath [ 0 ] != 0 ); in KDBVMakeSubPath() 886 if ( subpath [ 0 ] == '.' || subpath [ 1 ] == '/' ) in KDBVMakeSubPath() 897 subpath -= ns_size + 1; in KDBVMakeSubPath() 898 memmove ( subpath, ns, ns_size ); in KDBVMakeSubPath() 899 subpath [ ns_size ] = '/'; in KDBVMakeSubPath() 908 char *subpath, size_t subpath_max, const char *ns, in KDBMakeSubPath() argument [all …]
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H A D | wkdb-priv.h | 130 char *subpath, size_t subpath_max, const char *ns, 136 char *subpath, size_t subpath_max, const char *ns,
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H A D | wkdb.c | 1038 char *subpath, size_t subpath_max, const char *ns, in KDBVMakeSubPath() argument 1045 subpath += ns_size + 1; in KDBVMakeSubPath() 1053 subpath, subpath_max, path, args ); in KDBVMakeSubPath() 1056 int sz = vsnprintf ( subpath, subpath_max, path, args ); in KDBVMakeSubPath() 1070 assert ( subpath [ 0 ] != 0 ); in KDBVMakeSubPath() 1071 if ( subpath [ 0 ] == '.' || subpath [ 1 ] == '/' ) in KDBVMakeSubPath() 1082 subpath -= ns_size + 1; in KDBVMakeSubPath() 1083 memmove ( subpath, ns, ns_size ); in KDBVMakeSubPath() 1084 subpath [ ns_size ] = '/'; in KDBVMakeSubPath() 1093 char *subpath, size_t subpath_max, const char *ns, in KDBMakeSubPath() argument [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/fuse/ |
H A D | directory.c | 147 DirNodeChild* n = (DirNodeChild*)BSTreeFind(&cself->children, subpath, finder); in DirectoryNode_IsChild() 253 if( subpath != NULL && (rc = DirectoryNode_Lock(cself, false)) == 0 ) { in DirectoryNode_Attr() 265 const char* path = subpath ? subpath : "."; in DirectoryNode_Attr() 275 if( children == false || subpath != NULL ) { in DirectoryNode_Attr() 295 } else if( subpath != NULL ) { in DirectoryNode_Attr() 298 if( subpath == NULL && cself->mtime != 0 ) { in DirectoryNode_Attr() 321 if( subpath == NULL ) { in DirectoryNode_Dir() 359 DEBUG_LINE(8, "Listing kdir path %s/%s", cself->path, subpath); in DirectoryNode_Dir() 376 if( subpath == NULL ) { in DirectoryNode_Link() 380 DEBUG_LINE(8, "Resolving %s/%s", cself->path, subpath); in DirectoryNode_Link() [all …]
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H A D | file.c | 54 rc_t FileNode_Attr(const FileNode* cself, const char* subpath, uint32_t* type, KTime_t* ts, uint64_… in FileNode_Attr() argument 59 if( subpath != NULL ) { in FileNode_Attr() 86 rc_t FileNode_Link(const FileNode* cself, const char* subpath, char* buf, size_t buf_sz) in FileNode_Link() argument 99 rc_t FileNode_Open(const FileNode* cself, const char* subpath, const SAccessor** accessor) in FileNode_Open() argument 103 if( subpath != NULL ) { in FileNode_Open()
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H A D | node.c | 200 DEBUG_MSG(10, ("%s: %s/%s\n", __func__, cself->name, subpath)); in FSNode_Attr() 202 rc = cself->vtbl->Attr(cself, subpath, type, ts, file_sz, access, block_sz); in FSNode_Attr() 210 rc_t FSNode_Dir(const FSNode* cself, const char* subpath, FSNode_Dir_Visit func, void* data) in FSNode_Dir() argument 217 DEBUG_MSG(10, ("%s: %s/%s\n", __func__, cself->name, subpath)); in FSNode_Dir() 219 rc = cself->vtbl->Dir(cself, subpath, func, data); in FSNode_Dir() 227 rc_t FSNode_Link(const FSNode* cself, const char* subpath, char* buf, size_t buf_sz) in FSNode_Link() argument 234 DEBUG_MSG(10, ("%s: %s/%s\n", __func__, cself->name, subpath)); in FSNode_Link() 236 rc = cself->vtbl->Link(cself, subpath, buf, buf_sz); in FSNode_Link() 245 rc_t FSNode_Open(const FSNode* cself, const char* subpath, const SAccessor** accessor) in FSNode_Open() argument 252 DEBUG_MSG(10, ("%s: %s/%s\n", __func__, cself->name, subpath)); in FSNode_Open() [all …]
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H A D | node.h | 62 …rc_t (*Attr)(const FSNODE_IMPL* cself, const char* subpath, uint32_t* type, KTime_t* ts, uint64_t*… 65 rc_t (*Dir)(const FSNODE_IMPL* cself, const char* subpath, FSNode_Dir_Visit func, void* data); 68 rc_t (*Link)(const FSNODE_IMPL* cself, const char* subpath, char* buf, size_t buf_sz); 71 rc_t (*Open)(const FSNODE_IMPL* cself, const char* subpath, const SAccessor** accessor); 97 rc_t FSNode_Attr(const FSNode* cself, const char* subpath, uint32_t* type, KTime_t* ts, 100 rc_t FSNode_Dir(const FSNode* cself, const char* subpath, FSNode_Dir_Visit func, void* data); 102 rc_t FSNode_Link(const FSNode* cself, const char* subpath, char* buf, size_t buf_sz); 104 rc_t FSNode_Open(const FSNode* cself, const char* subpath, const SAccessor** accessor);
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H A D | remote-directory.c | 121 rc_t DirectoryNode_IsChild(const DirectoryNode* cself, const char* subpath, const FSNode** node, in DirectoryNode_IsChild() argument 124 DirNodeChild* n = (DirNodeChild*)BSTreeFind(&cself->children, subpath, finder); in DirectoryNode_IsChild() 144 if( subpath != NULL && (rc = DirectoryNode_Lock(cself, false)) == 0 ) { in DirectoryNode_Attr() 156 const char* path = subpath ? subpath : "."; in DirectoryNode_Attr() 166 if( children == false || subpath != NULL ) { in DirectoryNode_Attr() 186 } else if( subpath != NULL ) { in DirectoryNode_Attr() 189 if( subpath == NULL && cself->mtime != 0 ) { in DirectoryNode_Attr() 212 if( subpath == NULL ) { in DirectoryNode_Dir() 250 DEBUG_LINE(8, "Listing kdir path %s/%s", cself->path, subpath); in DirectoryNode_Dir() 264 if( subpath == NULL ) { in DirectoryNode_Open() [all …]
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H A D | remote-file.c | 56 rc_t RemoteFileNode_Attr(const RemoteFileNode* cself, const char* subpath, uint32_t* type, KTime_t*… in RemoteFileNode_Attr() argument 60 if( subpath != NULL ) { in RemoteFileNode_Attr() 79 const char* subpath, in RemoteFileNode_Open() argument 85 if( subpath != NULL ) { in RemoteFileNode_Open()
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H A D | remote-fuser.c | 42 const char* subpath; member 55 rc = XML_FindLock(path, recur, &request->node, &request->subpath); in SRequestMake() 153 rc = FSNode_Dir(request.node, request.subpath, func, data); in SRA_FUSER_GetDir() 165 rc = FSNode_Attr(request.node, request.subpath, type, ts, file_sz, access, block_sz); in SRA_FUSER_GetAttr() 177 rc = FSNode_Link(request.node, request.subpath, buf, buf_sz); in SRA_FUSER_ResolveLink() 189 rc = FSNode_Open(request.node, request.subpath, (const SAccessor**)data); in SRA_FUSER_OpenNode()
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H A D | remote-link.c | 63 rc_t RemoteLinkNode_Attr(const RemoteLinkNode* cself, const char* subpath, uint32_t* type, KTime_t*… in RemoteLinkNode_Attr() argument 67 if( subpath != NULL ) { in RemoteLinkNode_Attr() 86 const char* subpath, in RemoteLinkNode_Link() argument 93 if( subpath != NULL ) { in RemoteLinkNode_Link()
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H A D | remote-xml.c | 94 rc_t XML_FindLock(const char* path, bool recur, const FSNode** node, const char** subpath) in XML_FindLock() argument 102 if( path == NULL || node == NULL || subpath == NULL ) { in XML_FindLock() 153 *subpath = (p0 && p0[0] != '\0') ? p0 : NULL; in XML_FindLock() 158 DEBUG_MSG(10, ("Found: '%s', sub '%s'\n", nm, *subpath)); in XML_FindLock() 226 rc_t RootNode_Attr(const FSNode* cself, const char* subpath, uint32_t* type, KTime_t* ts, uint64_t*… in RootNode_Attr() argument 231 if( subpath != NULL ) { in RootNode_Attr() 238 rc_t RootNode_Dir(const FSNode* cself, const char* subpath, FSNode_Dir_Visit func, void* data) in RootNode_Dir() argument 240 if( subpath != NULL ) { in RootNode_Dir()
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H A D | remote-xml.h | 45 rc_t XML_FindLock(const char* path, bool recur, const FSNode** node, const char** subpath);
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H A D | sra-directory.c | 52 rc_t SRADirectoryNode_Attr(const SRADirectoryNode* cself, const char* subpath, uint32_t* type, KTim… in SRADirectoryNode_Attr() argument 56 if( subpath != NULL ) { in SRADirectoryNode_Attr() 66 rc_t SRADirectoryNode_Dir(const SRADirectoryNode* cself, const char* subpath, FSNode_Dir_Visit func… in SRADirectoryNode_Dir() argument 68 if( subpath != NULL ) { in SRADirectoryNode_Dir()
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