| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/ |
| H A D | ContigAlignmentsModifierUnitTest.java | 34 final Cigar cigar = TextCigarCodec.decode("56S27M15I32M21S"); in testGappedAlignmentBreaker_OneInsertion() local
52 final Cigar cigar = TextCigarCodec.decode("2S205M2D269M77S"); in testGappedAlignmentBreaker_OneDeletion() local
70 final Cigar cigar = TextCigarCodec.decode("397S118M2D26M6I50M7I26M1I8M13D72M398S"); in testGappedAlignmentBreaker_Complex() local
102 final Cigar cigar = TextCigarCodec.decode("10M10D10M60I10M10I10M50D10M"); in testGappedAlignmentBreaker_GapSizeSensitivity() local
125 final Cigar cigar = TextCigarCodec.decode("1H2S3M5I10M20D6M7S8H"); in testGappedAlignmentBreaker_HardAndSoftClip() local
148 Cigar cigar = TextCigarCodec.decode("10I10M5I10M"); in testGappedAlignmentBreaker_TerminalInsertionOperatorToSoftClip() local
187 Cigar cigar = TextCigarCodec.decode("10H20S30I40M50I60S70H"); in testGappedAlignmentBreaker_TerminalInsertionNeighboringClippings() local
218 final Cigar cigar = TextCigarCodec.decode("10S1044M122I395M75I"); in testGappedAlignmentBreaker_NegativeStrand() local
252 …private static Iterable<AlignmentInterval> willThrowOnInvalidCigar(final Cigar cigar, final int re… in willThrowOnInvalidCigar()
265 Cigar cigar = TextCigarCodec.decode("10H10I10M"); in testGappedAlignmentBreaker_NoLongerExpectException() local
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/mason2/ |
| H A D | mason_tests.cpp | 47 TCigarString cigar; in SEQAN_DEFINE_TEST() local
58 TCigarString cigar; in SEQAN_DEFINE_TEST() local
69 TCigarString cigar; in SEQAN_DEFINE_TEST() local
80 TCigarString cigar; in SEQAN_DEFINE_TEST() local
96 TCigarString cigar; in SEQAN_DEFINE_TEST() local
108 TCigarString cigar; in SEQAN_DEFINE_TEST() local
120 TCigarString cigar; in SEQAN_DEFINE_TEST() local
132 TCigarString cigar; in SEQAN_DEFINE_TEST() local
149 TCigarString cigar; in SEQAN_DEFINE_TEST() local
159 TCigarString cigar; in SEQAN_DEFINE_TEST() local
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| H A D | simulate_sanger.cpp | 54 TCigarString const & cigar) in _simulateSequence()
141 TCigarString cigar; in simulateRead() local
194 void SangerSequencingSimulator::_simulateCigar(TCigarString & cigar, unsigned sampleLength) in _simulateCigar()
240 TQualities & quals, TCigarString const & cigar, unsigned sampleLength) in _simulateQualities()
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| /dports/biology/py-crossmap/CrossMap-0.5.4/lib/cmmodule/ |
| H A D | bam_cigar.py | 32 def fetch_exon(chrom, st, cigar): argument
55 def fetch_intron(chrom, st, cigar): argument
78 def fetch_clip(chrom, st, cigar): argument
101 def fetch_deletion(chrom, st, cigar): argument
124 def fetch_insertion(chrom, st, cigar): argument
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | CigarUtils.java | 40 public static Cigar invertCigar (final Cigar cigar) { in invertCigar()
79 public static Cigar removeClipsAndPadding(final Cigar cigar) { in removeClipsAndPadding()
270 public static int countUnclippedReadBases(final Cigar cigar) { in countUnclippedReadBases()
284 …public static int countClippedBases(final Cigar cigar, final Tail tail, final CigarOperator typeOf… in countClippedBases()
311 public static int countClippedBases(final Cigar cigar, final Tail tail) { in countClippedBases()
318 public static int countClippedBases(final Cigar cigar, final CigarOperator clippingType) { in countClippedBases()
325 public static int countClippedBases(final Cigar cigar) { in countClippedBases()
329 public static int countAlignedBases(final Cigar cigar ) { in countAlignedBases()
359 …public static Cigar clipCigar(final Cigar cigar, final int start, final int stop, CigarOperator cl… in clipCigar()
406 public static int alignmentStartShift(final Cigar cigar, final int numClipped) { in alignmentStartShift()
[all …]
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| H A D | ArtificialReadUtils.java | 231 public static GATKRead createArtificialRead(final SAMFileHeader header, final Cigar cigar) { in createArtificialRead()
235 public static GATKRead createArtificialRead(final Cigar cigar) { in createArtificialRead()
242 public static GATKRead createUniqueArtificialRead(final Cigar cigar) { in createUniqueArtificialRead()
246 public static GATKRead createArtificialRead(final Cigar cigar, final String name) { in createArtificialRead()
455 … public static SAMRecord createArtificialSAMRecord(final SAMFileHeader header, final Cigar cigar) { in createArtificialSAMRecord()
459 public static SAMRecord createArtificialSAMRecord(final Cigar cigar) { in createArtificialSAMRecord()
467 public static SAMRecord createUniqueArtificialSAMRecord(final Cigar cigar) { in createUniqueArtificialSAMRecord()
538 Cigar cigar = new Cigar(cigarElements); in createRandomRead() local
670 final Cigar cigar = TextCigarCodec.decode(cigarString); in createSplicedInsertionPileupElement() local
725 final Cigar cigar = TextCigarCodec.decode(cigarString); in createSplicedDeletionPileupElement() local
[all …]
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| H A D | AlignmentUtils.java | 424 final Cigar cigar = r.getCigar(); in getNumAlignmentBlocks() local
447 final Cigar cigar = r.getCigar(); in getNumAlignedBasesCountingSoftClips() local
469 final Cigar cigar = r.getCigar(); in getNumHardClippedBases() local
492 final Cigar cigar = read.getCigar(); in countHighQualitySoftClips() local
605 public static boolean isInsideDeletion(final Cigar cigar, final int offset) { in isInsideDeletion()
651 public static byte[] readToAlignmentByteArray(final Cigar cigar, final byte[] read) { in readToAlignmentByteArray()
733 …public static CigarBuilder.Result leftAlignIndels(final Cigar cigar, final byte[] ref, final byte[… in leftAlignIndels()
941 public static boolean startsOrEndsWithInsertionOrDeletion(final Cigar cigar) { in startsOrEndsWithInsertionOrDeletion()
961 …public static CigarBuilder.Result trimCigarByReference(final Cigar cigar, final int start, final i… in trimCigarByReference()
973 …public static CigarBuilder.Result trimCigarByBases(final Cigar cigar, final int start, final int e… in trimCigarByBases()
[all …]
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| H A D | CigarBuilder.java | 194 final Cigar cigar = make(); in makeAndRecordDeletionsRemovedResult() local
199 private Cigar cigar; field in CigarBuilder.Result
203 …public Result(final Cigar cigar, final int leadingDeletionBasesRemoved, final int trailingDeletion… in Result()
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| /dports/biology/stacks/stacks-2.4/src/ |
| H A D | aln_utils.cc | 65 invert_cigar(string cigar) in invert_cigar()
78 invert_cigar(Cigar &cigar) in invert_cigar()
91 convert_local_cigar_to_global(Cigar &cigar) in convert_local_cigar_to_global()
183 parse_cigar(const char *cigar_str, Cigar &cigar, bool check_correctness) in parse_cigar()
227 apply_cigar_to_seq(const char *seq, const Cigar &cigar) in apply_cigar_to_seq()
281 apply_cigar_to_model_seq(const char *seq, const Cigar &cigar) in apply_cigar_to_model_seq()
335 apply_cigar_to_seq(char *seq, uint seq_len, const char *old_seq, Cigar &cigar) in apply_cigar_to_seq()
387 apply_cigar_to_model_seq(char *seq, uint seq_len, const char *model, Cigar &cigar) in apply_cigar_to_model_seq()
439 remove_cigar_from_seq(const char *seq, const Cigar &cigar) in remove_cigar_from_seq()
485 std::tuple<uint,uint,uint> cigar_lengths(const Cigar& cigar) { in cigar_lengths()
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| H A D | BamI.cc | 86 uint32_t* cigar = (uint32_t*)(r_->data + r_->core.l_qname); in assign() local
258 Cigar cigar = rec.cigar(); in next_seq() local
295 bam_find_start_bp(int aln_bp, strand_type strand, const Cigar& cigar) in bam_find_start_bp()
332 bam_edit_gaps(const Cigar& cigar, char *seq) in bam_edit_gaps()
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| /dports/biology/pbbam/pbbam-0.18.0/tests/src/ |
| H A D | test_BamRecordImplVariableData.cpp | 175 Cigar cigar; in TEST() local
188 const std::string cigar = "100="; in TEST() local
199 const std::string cigar = "100="; in TEST() local
212 const std::string cigar = "100="; in TEST() local
225 const std::string cigar = "100="; in TEST() local
1129 const std::string cigar = ""; in TEST() local
1395 const std::string cigar = ""; in TEST() local
2179 const std::string cigar = ""; in TEST() local
2353 const std::string cigar = ""; in TEST() local
3526 const std::string cigar = ""; in TEST() local
[all …]
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| H A D | test_Cigar.cpp | 89 Cigar cigar = Cigar::FromStdString(emptyCigar); in TEST() local
97 Cigar cigar = Cigar::FromStdString(singleCigar); in TEST() local
109 Cigar cigar = Cigar::FromStdString(multiCigar); in TEST() local
136 Cigar cigar; in TEST() local
144 Cigar cigar; in TEST() local
154 Cigar cigar; in TEST() local
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| H A D | test_BamRecord.cpp | 82 const std::string& cigar, in MakeCigaredImpl()
96 const std::string& cigar, in MakeCigaredRecord()
102 const std::string& cigar, in MakeCigaredBaseRecord()
117 const std::string& cigar, in MakeCigaredFrameRecord()
132 const std::string& cigar, in MakeCigaredQualRecord()
249 void CheckAlignAndClip(const std::string& cigar, in CheckAlignAndClip()
276 void CheckPulseDataAlignAndClip(const std::string& cigar, in CheckPulseDataAlignAndClip()
472 void CheckPulseBaseTags(const std::string& cigar, in CheckPulseBaseTags()
508 void CheckPulseFrameTags(const std::string& cigar, in CheckPulseFrameTags()
552 void CheckPulseQualityTags(const std::string& cigar, in CheckPulseQualityTags()
[all …]
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| H A D | test_LongCigar.cpp | 42 Cigar cigar; in SetLongCigar() local
52 static void CheckLongCigar(const Cigar& cigar) in CheckLongCigar()
89 const auto cigar = b.CigarData(); in TEST() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | CigarUtilsUnitTest.java | 256 public void testLeftClipFunkly(final Cigar cigar) { in testLeftClipFunkly()
261 public void testRightClipFunkly(final Cigar cigar) { in testRightClipFunkly()
288 public void testClipCounts(final Cigar cigar) { in testClipCounts()
327 public void testReadLength(final Cigar cigar) { in testReadLength()
438 final Cigar cigar = TextCigarCodec.decode(cigarString); in testAlignmentStartShift() local
447 final Cigar cigar = TextCigarCodec.decode("35H40S10M20I25M30D50M55S60H"); in createReadWalkDistanceTestDataException() local
468 …public void testReadWalkDistanceTestDataException(final Cigar cigar, final int startInclusive, fin… in testReadWalkDistanceTestDataException()
477 final Cigar cigar = TextCigarCodec.decode("35H40S10M20I25M30D50M55S60H"); in createReadWalkDistanceTestData() local
501 …public void testReadWalkDistanceTestData(final Cigar cigar, final int startInclusiveOnRead, final … in testReadWalkDistanceTestData()
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| H A D | AlignmentUtilsUnitTest.java | 78 private Haplotype makeHaplotypeForAlignedToRefTest(final String bases, final String cigar) { in makeHaplotypeForAlignedToRefTest()
351 public void testNumAlignedBasesCountingSoftClips(final Cigar cigar, final int expected) { in testNumAlignedBasesCountingSoftClips()
373 public void testNumHardClipped(final Cigar cigar, final int expected) { in testNumHardClipped()
400 public void testNumAlignedBlocks(final Cigar cigar, final int expected) { in testNumAlignedBlocks()
450 final StringBuilder cigar = new StringBuilder(); in testSoftClipsData() local
533 final StringBuilder cigar = new StringBuilder(); in buildTestCigarString() local
626 final Cigar cigar = new Cigar(cigarElements); in testIsInsideDeletion() local
899 final Cigar cigar = TextCigarCodec.decode(cigarString); in testTrimCigar() local
940 final Cigar cigar = TextCigarCodec.decode(cigarString); in testTrimCigarByBase() local
1118 … public void testStartsOrEndsWithInsertionOrDeletion(final String cigar, final boolean expected) { in testStartsOrEndsWithInsertionOrDeletion()
[all …]
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| /dports/biology/py-pysam/pysam-0.18.0/samtools/ |
| H A D | bam_color.c | 53 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCSi() local
82 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCQi() local
143 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCEi() local
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| H A D | bam_color.c.pysam.c | 55 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCSi() local
84 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCQi() local
145 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCEi() local
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| /dports/biology/samtools/samtools-1.14/ |
| H A D | bam_color.c | 53 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCSi() local
82 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCQi() local
143 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCEi() local
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| /dports/biology/pbbam/pbbam-0.18.0/tools/pbbamify/src/ |
| H A D | PbBamify.cpp | 110 for (const auto& cigar : cigarData) { in ConvertHardToSoftClipping() local
139 for (const auto& cigar : cigarData) { in SequenceLengthFromCigar() local
150 for (const auto& cigar : cigarData) { in CheckIsCigarBasic() local
173 for (const auto& cigar : cigarData) { in BasicToExtendedCigar() local
318 auto cigar = record.Impl().CigarData(); in AugmentAlignment() local
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/util/ |
| H A D | U2AssemblyUtils.cpp | 97 const char *cigar = cigarString.constData(); in parseCigar() local
117 QByteArray U2AssemblyUtils::cigar2String(const QList<U2CigarToken> &cigar) { in cigar2String()
131 qint64 U2AssemblyUtils::getCigarExtraLength(const QList<U2CigarToken> &cigar) { in getCigarExtraLength()
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| H A D | U2AssemblyReadIterator.cpp | 160 QList<U2CigarToken> cigar; in t01() local
188 QList<U2CigarToken> cigar; in t02() local
201 QList<U2CigarToken> cigar; in t03() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ |
| H A D | ReadPosRankSumTestUnitTest.java | 46 Cigar cigar = TextCigarCodec.decode("10M"); in makeRead() local
116 final Cigar cigar = TextCigarCodec.decode(cigarString); in testIsUsableRead() local
194 final Cigar cigar = TextCigarCodec.decode("10I10M"); in testLeadingInsertion() local
204 final Cigar cigar = TextCigarCodec.decode("10M10D1M10D10M"); in testSNPBetweenTwoDeletions() local
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| /dports/biology/emboss/EMBOSS-6.6.0/ajax/core/ |
| H A D | ajcigar.c | 137 AjPCigar ajCigarNewS(const AjPStr cigar) in ajCigarNewS()
195 AjPCigar cigar; in ajCigarDel() local
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| /dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/ |
| H A D | CigarHelper.cpp | 29 Cigar* cigar = record.getCigarInfo(); in softClipBeginByRefPos() local
189 Cigar* cigar = record.getCigarInfo(); in softClipEndByRefPos() local
|