| /dports/biology/bolt-lmm/BOLT-LMM_v2.3.4/src/ |
| H A D | FileUtils.hpp | 58 std::ifstream fin; member in FileUtils::AutoGzIfstream
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| H A D | MapInterpolater.cpp | 49 FileUtils::AutoGzIfstream fin; fin.openOrExit(geneticMapFile); in MapInterpolater() local
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| H A D | SnpData.cpp | 206 FileUtils::AutoGzIfstream fin; fin.openOrExit(famFile); in processIndivs() local
294 FileUtils::AutoGzIfstream fin; in processSnps() local
532 void SnpData::readBedLine(uchar genoLine[], uchar bedLineIn[], FileUtils::AutoGzIfstream &fin, in readBedLine()
660 FileUtils::AutoGzIfstream fin; in SnpData() local
770 FileUtils::AutoGzIfstream fin; fin.openOrExit(bimFile); in readBimFile() local
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| H A D | SpectrumTools.cpp | 75 FileUtils::AutoGzIfstream fin; fin.openOrExit(fileName); in readSpectrum() local
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| /dports/biology/bowtie2/bowtie2-2.4.4/ |
| H A D | bt2_io.cpp | 640 readEbwtRefnames(FILE* fin, EList<string>& refnames) { in readEbwtRefnames()
726 FILE* fin; in readEbwtRefnames() local
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| /dports/biology/cd-hit/cdhit-4.8.1/cd-hit-auxtools/ |
| H A D | bioSequence.cxx | 75 FILE *fin = inputFile; in Update() local
131 FILE *fin = fopen( file.Data(), "r" ); in ReadFastAQ() local
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| /dports/biology/cd-hit/cdhit-4.8.1/ |
| H A D | cdhit-common.c++ | 1695 gzFile fin = gzopen(file, "r"); in Readgz() local
1794 FILE *fin = fopen( file, "rb" ); in Read() local
1888 gzFile fin = gzopen(file, "r"); in Readgz() local
2048 FILE *fin = fopen( file, "rb" ); in Read() local
2309 FILE *fin = fopen( db, "rb" ); in DivideSave() local
2351 gzFile fin = gzopen(db, "r"); in WriteClustersgz() local
2393 FILE *fin = fopen( db, "rb" ); in WriteClusters() local
2429 gzFile fin = gzopen(db, "r"); in WriteClustersgz() local
2517 FILE *fin = fopen( db, "rb" ); in WriteClusters() local
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| /dports/biology/emboss/EMBOSS-6.6.0/ajax/core/ |
| H A D | ajfmt.c | 2497 AjBool fin = ajFalse; in fmtVfscanf() local
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| /dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
| H A D | recoder.c | 396 AjPFile fin = NULL; /* file pointer to RE file data */ in recoder_readRE() local
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| H A D | silent.c | 401 AjPFile fin = NULL; in silent_restr_read() local
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| /dports/biology/fasta/fasta/ |
| H A D | fromgb.c | 40 FILE *fin, *fout; variable
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| H A D | res_stats.c | 64 FILE *fin; local
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| /dports/biology/fasta3/fasta-36.3.8/src/ |
| H A D | res_stats.c | 100 FILE *fin; local
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/test/ |
| H A D | hfile.c | 81 hFILE *fin = NULL; variable
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| H A D | sam.c | 1463 FILE *fin, *fout; in faidx1() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/funcotator/filtrationRules/ |
| H A D | AlleleFrequencyGnomadUtils.java | 32 fin, // Finnish enumConstant
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| /dports/biology/graphlan/nsegata-graphlan-66ec7cfce81e/pyphlan/ |
| H A D | tab.py | 8 def __init__( self, fin = sys.stdin, sep = "\t" ): argument
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| /dports/biology/graphlan/nsegata-pyphlan-eae40ebc0030/ |
| H A D | tab.py | 8 def __init__( self, fin = sys.stdin, sep = "\t" ): argument
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| /dports/biology/hhsuite/hh-suite-3.3.0/src/cs/ |
| H A D | alignment-inl.h | 30 Alignment<Abc>::Alignment(FILE* fin, AlignmentFormat format) { in Alignment()
109 void Alignment<Abc>::Read(FILE* fin, AlignmentFormat format) { in Read()
160 void Alignment<Abc>::ReadFastaFlavors(FILE* fin, std::vector<std::string>& headers, std::vector<std… in ReadFastaFlavors()
212 void Alignment<Abc>::ReadPsi(FILE* fin, std::vector<std::string>& headers, std::vector<std::string>… in ReadPsi()
264 void Alignment<Abc>::ReadFasta(FILE* fin, in ReadFasta()
275 void Alignment<Abc>::ReadA2M(FILE* fin, std::vector<std::string>& headers, std::vector<std::string>… in ReadA2M()
280 void Alignment<Abc>::ReadA3M(FILE* fin, std::vector<std::string>& headers, std::vector<std::string>… in ReadA3M()
670 void ReadAll(FILE* fin, AlignmentFormat format, std::vector< Alignment<Abc> >& v) { in ReadAll()
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| H A D | context_library-inl.h | 35 ContextLibrary<Abc>::ContextLibrary(FILE* fin) in ContextLibrary()
48 void ContextLibrary<Abc>::Read(FILE* fin) { in Read()
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| H A D | context_profile-inl.h | 40 ContextProfile<Abc>::ContextProfile(FILE* fin) { Read(fin); } in ContextProfile()
81 void ContextProfile<Abc>::Read(FILE* fin) { in Read()
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| H A D | count_profile-inl.h | 62 void CountProfile<Abc>::Read(FILE* fin) { in Read()
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| H A D | crf-inl.h | 35 Crf<Abc>::Crf(FILE* fin) in Crf()
54 void Crf<Abc>::Read(FILE* fin) { in Read()
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| H A D | crf_state-inl.h | 28 void CrfState<Abc>::Read(FILE* fin) { in Read()
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| H A D | cstranslate_app.h | 136 FILE *fin; in Run() local
437 FILE *fin; in SetupPseudocountEngine() local
474 FILE *fin; in SetupAbstractStateEngine() local
547 void ReadProfile(FILE *fin, string &header, CountProfile<Abc> &profile) { in ReadProfile()
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