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Functions854 in github.com/Illumina/hap.py

⨍ Functions 854◇ Types & classes 237

MethodXCMPQuantify

src/c++/lib/quantify/XCmpQuantify.cpp:41

src/c++/include/RefVar.hh:57

src/python/Somatic/__init__.py:28

reads in a BED file and converts it to an interval tree for searching

src/python/Tools/bedintervaltree.py:18

src/python/Tools/vcfcallerinfo.py:24

src/python/Tools/__init__.py:108

Make a subprocess for bgzip :param filename: name of the output file :param force: true to overwrite if file exists

src/python/Tools/__init__.py:179

src/python/Tools/roc.py:82

src/python/Tools/bedintervaltree.py:31

src/python/Tools/vcfcallerinfo.py:30

src/python/Tools/bedintervaltree.py:28

Method_branchpoint

src/c++/lib/diploidgraphs/GraphReference.cpp:560

Method_n2clookup

src/c++/lib/variant/VariantStatistics.cpp:186

* @brief add counts */

src/c++/lib/variant/VariantStatistics.cpp:450

enqueue a set of variants */

src/c++/lib/variant/VariantLocationAggregator.cpp:95

enqueue a set of variants */

src/c++/lib/variant/VariantPrimitiveSplitter.cpp:125

enqueue a set of variants */

src/c++/lib/variant/VariantAlleleUniq.cpp:82

enqueue a set of variants */

src/c++/lib/variant/VariantAlleleSplitter.cpp:92

enqueue a set of variants */

src/c++/lib/variant/VariantHomrefSplitter.cpp:104

enqueue a set of variants */

src/c++/lib/variant/VariantAlleleNormalizer.cpp:152

enqueue a set of variants */

src/c++/lib/variant/VariantCallsOnly.cpp:101

enqueue a set of variants */

src/c++/lib/variant/VariantLeftPadding.cpp:116

* Add a BCF record. Will duplicate the record and keep the copy * @param v bcf record */

src/c++/lib/scmp/BlockAlleleCompare.cpp:157

Variant input **/ enqueue a set of variants */

src/c++/include/variant/VariantAlleleRemover.hh:59

Variant input **/ enqueue a set of variants */

src/c++/include/variant/VariantTee.hh:69

Variant input **/ enqueue a set of variants */

src/c++/include/variant/VariantTee.hh:130

MethodaddComment

external/jsoncpp/jsoncpp.cpp:536

external/jsoncpp/jsoncpp.cpp:904

MethodaddErrorAndRecover

external/jsoncpp/jsoncpp.cpp:927

MethodaddPathInArg

external/jsoncpp/jsoncpp.cpp:2962

MethodaddROCValue

add ROC decision point

src/c++/lib/quantify/BlockQuantify.cpp:134

MethodaddSample

src/c++/lib/variant/VariantWriter.cpp:129

FunctionaddToLocationMap

src/c++/lib/variant/VariantLocationMap.cpp:269

Methodadd_homref

enqueue homref block */

src/c++/lib/variant/VariantProcessor.cpp:192

Methodadd_variant

enqueue a RefVar */

src/c++/lib/variant/VariantProcessor.cpp:168

* @brief Advance one line * @return true if a variant was retrieved, false otherwise */

src/c++/lib/variant/VariantLocationAggregator.cpp:366

* @brief Advance one line * @return true if a variant was retrieved, false otherwise */

src/c++/lib/variant/VariantPrimitiveSplitter.cpp:161

* @brief Advance one line * @return true if a variant was retrieved, false otherwise */

src/c++/lib/variant/VariantAlleleUniq.cpp:174

* @brief Advance one line * @return true if a variant was retrieved, false otherwise */

src/c++/lib/variant/VariantAlleleSplitter.cpp:123

* @brief Advance one line * @return true if a variant was retrieved, false otherwise */

src/c++/lib/variant/VariantHomrefSplitter.cpp:131

* @brief Advance one line * @return true if a variant was retrieved, false otherwise */

src/c++/lib/variant/VariantAlleleNormalizer.cpp:305

* @brief Advance one line * @return true if a variant was retrieved, false otherwise */

src/c++/lib/variant/VariantLeftPadding.cpp:143

src/c++/lib/diploidgraphs/DiploidReference.cpp:310

* @brief Advance one line * @return true if a variant was retrieved, false otherwise */

src/c++/include/variant/VariantAlleleRemover.hh:78

* @brief Advance one line * @return true if a variant was retrieved, false otherwise */

src/c++/include/variant/VariantTee.hh:94

* @brief Advance one line * @return true if a variant was retrieved, false otherwise */

src/c++/include/variant/VariantTee.hh:149

external/jsoncpp/jsoncpp.cpp:215

MethodallHomref

return if all calls are homref */

src/c++/include/Variant.hh:203

allocate space for an array of objectPerAllocation object. @warning it is the responsability of the caller to call objects constructors.

external/jsoncpp/jsoncpp.cpp:1099

MethodallocateBatch

external/jsoncpp/jsoncpp.cpp:1144

MethodasConstString

external/jsoncpp/jsoncpp.cpp:2121

external/jsoncpp/jsoncpp.cpp:2172

external/jsoncpp/jsoncpp.cpp:2148

Methodbcf_get_gts

src/c++/lib/tools/BCFHelpers.cpp:168

Methodbcf_get_info

src/c++/lib/tools/BCFHelpers.cpp:207

Methodbcf_get_numeric_format

src/c++/lib/tools/BCFHelpers.cpp:61

FunctionblocksplitWrapper

(location_str, args)

src/python/Haplo/blocksplit.py:27

FunctionblocksplitWrapper

Blocksplit for partial credit preprocessing

src/python/Haplo/partialcredit.py:95

translate count key to name */

src/c++/lib/variant/VariantStatistics.cpp:175

external/jsoncpp/json/json.h:419

MethodcheckAndScore

* update / optimize assignments * * return < true/false if assignment produces match, number of matched variants > * Total number of va

src/c++/lib/scmp/DistanceBasedMatcher.cpp:99

Return a data frame with features collected from the given VCF, tagged by given type

src/python/Somatic/__init__.py:57

Return a data frame with features collected from the given VCF, tagged by given type

src/python/Somatic/__init__.py:104

Return a data frame with features collected from the given VCF, tagged by given type

src/python/Somatic/__init__.py:136

Return a data frame with features collected from the given VCF, tagged by given type

src/python/Somatic/__init__.py:149

Return a data frame with features collected from the given VCF, tagged by given type

src/python/Somatic/__init__.py:163

Return a data frame with features collected from the given VCF, tagged by given type

src/python/Somatic/__init__.py:177

Return a data frame with features collected from the given VCF, tagged by given type

src/python/Somatic/__init__.py:191

Return a data frame with features collected from the given VCF, tagged by given type

src/python/Somatic/__init__.py:206

Return a data frame with features collected from the given VCF, tagged by given type

src/python/Somatic/__init__.py:221

Return a data frame with features collected from the given VCF, tagged by given type

src/python/Somatic/__init__.py:235

Return a data frame with features collected from the given VCF, tagged by given type

src/python/Somatic/__init__.py:250

MethodcomputeDistance

external/jsoncpp/jsoncpp.cpp:1274

MethodcontigNonNSize

* return the non-N padded size of a contig. This is calculated * as the size of the contig minus any N's at the beginning or * at the end.

src/c++/lib/tools/Fasta.cpp:284

MethodcontigSize

* return the size of a contig. Sum of all contig sizes if contig == 0 * @param contig name of contig, or empty * @return number of bases in

src/c++/lib/tools/Fasta.cpp:253

Return number of records per label :param label: string label :return: number of intervals which have the given label

src/python/Tools/bedintervaltree.py:87

FunctioncountVCFRows

Count the number of rows in a VCF :param filename: VCF file name :return: number of rows

src/python/Tools/bcftools.py:82

MethodcountVariants

src/c++/lib/quantify/XCmpQuantify.cpp:121

MethodcountVariants

src/c++/lib/quantify/GA4GHQuantify.cpp:91

MethoddecodeDouble

external/jsoncpp/jsoncpp.cpp:738

MethoddecodeNumber

external/jsoncpp/jsoncpp.cpp:680

MethoddecodeString

external/jsoncpp/jsoncpp.cpp:784

MethoddecodeUnicodeCodePoint

external/jsoncpp/jsoncpp.cpp:847

MethoddecodeUnicodeEscapeSequence

external/jsoncpp/jsoncpp.cpp:876

Methoddecrement

external/jsoncpp/jsoncpp.cpp:1261

FunctiondefaultReference

src/python/Tools/__init__.py:29

src/c++/lib/variant/Variant.cpp:272

MethoddropNullPlaceholders

external/jsoncpp/jsoncpp.cpp:3234

src/c++/include/helpers/LocationInfo.hh:276

MethodenableYAMLCompatibility

external/jsoncpp/jsoncpp.cpp:3232

Methodensure_is_interval

src/c++/include/helpers/IntervalList.hh:278

Functionerror_stop

src/c++/include/Error.hh:58

MethodexpectToken

external/jsoncpp/jsoncpp.cpp:414

MethodextraCount

src/c++/lib/variant/VariantStatistics.cpp:328

MethodextraCountsToBI

src/c++/lib/variant/VariantStatistics.cpp:659

FunctionfastaNonNContigLengths

Return contig lengths in a fasta file excluding Ns in the beginning or end

src/python/Tools/fastasize.py:50

FunctionfindVCFEval

Return default version of rtgtools if hap.py was built with rtgtools included.

src/python/Haplo/vcfeval.py:30

empty internal buffer */

src/c++/lib/variant/VariantLocationAggregator.cpp:381

empty internal buffer */

src/c++/lib/variant/VariantPrimitiveSplitter.cpp:546

empty internal buffer */

src/c++/lib/variant/VariantAlleleUniq.cpp:189

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