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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/
H A DReadsSparkSinkUnitTest.java130 final java.nio.file.Path subpath = defaultPartsDir.resolve("subpath"); in testSpecifyPartsDir() local
135 Files.createFile(subpath); in testSpecifyPartsDir()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/align/nw/
H A Dmm_aligner.hpp96 list<ETranscriptSymbol>& subpath);
114 list<ETranscriptSymbol>& subpath) const;
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/nw/
H A Dmm_aligner.cpp371 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 …]
/dports/biology/ncbi-toolkit/ncbi/link/macmet/
H A Dsetrsrc.c306 static void RecurseDir (char * directory, char * subpath) in RecurseDir() argument
315 MyFileBuildPath (path, subpath, NULL); in RecurseDir()
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/kdb/
H A Dkdb-priv.h103 char *subpath, size_t subpath_max, const char *ns,
109 char *subpath, size_t subpath_max, const char *ns,
H A Dkdb.c853 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
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H A Dwkdb-priv.h130 char *subpath, size_t subpath_max, const char *ns,
136 char *subpath, size_t subpath_max, const char *ns,
H A Dwkdb.c1038 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
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/dports/biology/p5-Bio-Glite/Bio-Glite-0.10/inc/Module/
H A DInstall.pm239 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: $!";
/dports/biology/p5-Bio-MAGETAB/Bio-MAGETAB-1.31/inc/Module/
H A DInstall.pm328 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');
/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/kdb/
H A Dkdb-priv.h103 char *subpath, size_t subpath_max, const char *ns,
109 char *subpath, size_t subpath_max, const char *ns,
H A Dkdb.c853 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
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H A Dwkdb-priv.h130 char *subpath, size_t subpath_max, const char *ns,
136 char *subpath, size_t subpath_max, const char *ns,
H A Dwkdb.c1038 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 …]
/dports/biology/sra-tools/sra-tools-2.11.0/tools/fuse/
H A Ddirectory.c147 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()
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H A Dfile.c54 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()
H A Dnode.c200 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()
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H A Dnode.h62 …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);
H A Dremote-directory.c121 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()
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H A Dremote-file.c56 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()
H A Dremote-fuser.c42 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()
H A Dremote-link.c63 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()
H A Dremote-xml.c94 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()
H A Dremote-xml.h45 rc_t XML_FindLock(const char* path, bool recur, const FSNode** node, const char** subpath);
H A Dsra-directory.c52 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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