Index

A

AddsMarks (FlaggerADF attribute) (FlaggerALF attribute) (FlaggerDVF attribute) (FlaggerLQF attribute) (ReadAwareProcess attribute) (ReadAwareProcessProtocol attribute) (TaggerDupmark attribute) (TaggerLowQual attribute) (TaggerOverlap attribute) (TaggerSupporting attribute) AlignmentScoreTest (class in hairpin2.sci_funcs)

AlignmentScoreTest.ResultPack (class in hairpin2.sci_funcs) AlignmentScoreTest.ResultPack.Info (class in hairpin2.sci_funcs) all (ReadView property) ALL (ValidNucleotides attribute) alt (RunParamsShared attribute) ANOMALOUS_DISTRIBUTION (FlaggerNamespaces attribute) AnomalousDistributionTest (class in hairpin2.sci_funcs) AnomalousDistributionTest.ResultPack (class in hairpin2.sci_funcs) AnomalousDistributionTest.ResultPack.Info (class in hairpin2.sci_funcs) avg_as (AlignmentScoreTest.ResultPack attribute) (ResultALF attribute) avg_AS_threshold (FixedParamsALF attribute)

B

BAD_OP (TagSupportingReads.SupportFlags attribute) BASEQUAL (TagLowQualReads.QualFlags attribute)

BOTH (Strand attribute) BOTH_STRAND_DISTRIB_BOTH (AnomalousDistributionTest.ResultPack.Info attribute) BOTH_STRAND_DISTRIB_ONE (AnomalousDistributionTest.ResultPack.Info attribute)

C

check_for_mates() (TagFragmentReads static method) check_low_qual_read() (TagLowQualReads class method) check_namespacing_clashfree() (RAExec static method) check_read_supporting() (TagSupportingReads class method) check_stutter_duplicates() (TagStutterDuplicateReads class method) CLEAR (TagLowQualReads.QualFlags attribute) (TagSupportingReads.SupportFlags attribute)

CLIPQUAL (TagLowQualReads.QualFlags attribute) ConfigError ConfigFile (class in hairpin2.infrastructure.cli) convert() (ConfigFile method) (JSONOrFile method) convert_pysam_to_extread() (ReadView static method)

D

DataExtensionBase (class in hairpin2.infrastructure.structures) DEL (MutTypes attribute)

DUPLICATION (FlaggerNamespaces attribute) duplication_window_size (FixedParamsDupmark attribute)

E

EDGE_CLUSTERING (AnomalousDistributionTest.ResultPack.Info attribute) edge_clustering_threshold (FixedParamsADF attribute) edge_definition (FixedParamsADF attribute) endpoints (TagStutterDuplicateReads.FragmentEndpoints attribute) EngineFactory (ReadAwareProcess attribute) (ReadAwareProcessProtocol attribute) EngineFactory() (FlaggerADF method) (FlaggerALF method) (FlaggerDVF method) (FlaggerLQF method) (TaggerDupmark method) (TaggerLowQual method) (TaggerOverlap method) (TaggerSupporting method)

exclude_marks (ReadAwareProcess property) (ReadAwareProcessProtocol property) ExecutorError ext_obj_has_mark() (in module hairpin2.infrastructure.structures) ExtendedRead (class in hairpin2.infrastructure.structures) ExtendedVariant (class in hairpin2.infrastructure.structures)

F

F (Strand attribute) FIELDS_MISSING (TagSupportingReads.SupportFlags attribute) fixed_params (ReadAwareProcess property) (ReadAwareProcessProtocol property) FixedParamClass (FlaggerADF attribute) (FlaggerALF attribute) (FlaggerDVF attribute) (FlaggerLQF attribute) (ReadAwareProcess attribute) (ReadAwareProcessProtocol attribute) (TaggerDupmark attribute) (TaggerLowQual attribute) (TaggerOverlap attribute) (TaggerSupporting attribute) FixedParams (class in hairpin2.infrastructure.process_params) FixedParamsADF (class in hairpin2.process_wrappers.ADF) FixedParamsALF (class in hairpin2.process_wrappers.ALF)

FixedParamsDupmark (class in hairpin2.process_wrappers.DVF) FixedParamsDVF (class in hairpin2.process_wrappers.DVF) FixedParamsLQF (class in hairpin2.process_wrappers.LQF) FLAGGER (ProcessKindEnum attribute) flagger_params (VariantFlaggerEngine property) FlaggerADF (class in hairpin2.process_wrappers.ADF) FlaggerALF (class in hairpin2.process_wrappers.ALF) FlaggerDVF (class in hairpin2.process_wrappers.DVF) FlaggerLQF (class in hairpin2.process_wrappers.LQF) FlaggerNamespaces (class in hairpin2.const) flaggers (RAExec property) FlagName (FlagResult attribute) (ResultADF attribute) (ResultALF attribute) (ResultDVF attribute) (ResultLQF attribute) FlagResult (class in hairpin2.infrastructure.structures) from_config() (RAExec class method)

G

getinfo() (FlagResult method) (ResultADF method) (ResultALF method) (ResultDVF method) (ResultLQF method)

H

hairpin2 module hairpin2() (in module hairpin2.main) hairpin2.const module hairpin2.infrastructure module hairpin2.infrastructure.cli module hairpin2.infrastructure.configure_funcs module hairpin2.infrastructure.process module hairpin2.infrastructure.process_engines module hairpin2.infrastructure.process_params module hairpin2.infrastructure.rascheduler module hairpin2.infrastructure.structures module

hairpin2.main module hairpin2.process_wrappers module hairpin2.process_wrappers.ADF module hairpin2.process_wrappers.ALF module hairpin2.process_wrappers.DVF module hairpin2.process_wrappers.LQF module hairpin2.process_wrappers.mark_overlap module hairpin2.process_wrappers.mark_support module hairpin2.process_wrappers.shared module hairpin2.sci_funcs module

I

Info (ResultPackProtocol attribute) info_flag (FlagResult attribute) InfoFlags (FlagResult attribute) (ResultADF attribute) (ResultALF attribute) (ResultDVF attribute) (ResultLQF attribute) InfoFlagsAllSet (FlagResult attribute) (ResultADF attribute) (ResultALF attribute) (ResultDVF attribute) (ResultLQF attribute)

INS (MutTypes attribute) INSUFFICIENT_AS_TAGS (AlignmentScoreTest.ResultPack.Info attribute) INSUFFICIENT_READS (AnomalousDistributionTest.ResultPack.Info attribute) items() (ReadView method)

J

JSONOrFile (class in hairpin2.infrastructure.cli)

K

keys() (ReadView method)

L

loss_ratio (ResultDVF attribute) (ResultLQF attribute)

low_n_supporting_reads_boundary (FixedParamsADF attribute) LOW_QUAL (FlaggerNamespaces attribute) LOW_QUAL_TAG (Tags attribute)

M

make_extended_read() (in module hairpin2.infrastructure.structures) make_read_processor() (in module hairpin2.infrastructure.configure_funcs) make_variant_flagger() (in module hairpin2.infrastructure.configure_funcs) mandate_excludes (RAExec property) MAPQUAL (TagLowQualReads.QualFlags attribute) mark_ext_obj() (in module hairpin2.infrastructure.structures) MARK_LOW_QUAL (TaggerNamespaces attribute) MARK_OVERLAP (TaggerNamespaces attribute) mark_read() (in module hairpin2.infrastructure.structures) MARK_STUTTER_DUP (TaggerNamespaces attribute) MARK_SUPPORT (TaggerNamespaces attribute) min_avg_clip_quality (QualParams attribute) min_base_quality (QualParams attribute) min_MAD_both_strand_strong (FixedParamsADF attribute) min_MAD_both_strand_weak (FixedParamsADF attribute) min_MAD_one_strand (FixedParamsADF attribute) min_mapping_quality (QualParams attribute) MIN_NON_EDGE (AnomalousDistributionTest.ResultPack.Info attribute) min_non_edge_reads (FixedParamsADF attribute) MIN_PASS (ProportionBasedTest.ResultPack.Info attribute) min_pass_reads (FixedParamsDVF attribute) (FixedParamsLQF attribute) min_sd_both_strand_strong (FixedParamsADF attribute) min_sd_both_strand_weak (FixedParamsADF attribute) min_sd_one_strand (FixedParamsADF attribute) model_config (FixedParams attribute) (FixedParamsADF attribute) (FixedParamsALF attribute) (FixedParamsDupmark attribute) (FixedParamsDVF attribute) (FixedParamsLQF attribute) (QualParams attribute) (RunParams attribute) (RunParamsShared attribute)

module hairpin2 hairpin2.const hairpin2.infrastructure hairpin2.infrastructure.cli hairpin2.infrastructure.configure_funcs hairpin2.infrastructure.process hairpin2.infrastructure.process_engines hairpin2.infrastructure.process_params hairpin2.infrastructure.rascheduler hairpin2.infrastructure.structures hairpin2.main hairpin2.process_wrappers hairpin2.process_wrappers.ADF hairpin2.process_wrappers.ALF hairpin2.process_wrappers.DVF hairpin2.process_wrappers.LQF hairpin2.process_wrappers.mark_overlap hairpin2.process_wrappers.mark_support hairpin2.process_wrappers.shared hairpin2.sci_funcs mut_type (RunParamsShared attribute) MutTypes (class in hairpin2.const)

N

NA (TestOutcomes attribute) name (ConfigFile attribute) NO_READS (AlignmentScoreTest.ResultPack.Info attribute) (AnomalousDistributionTest.ResultPack.Info attribute) (ProportionBasedTest.ResultPack.Info attribute) NODATA (AlignmentScoreTest.ResultPack.Info attribute) (AnomalousDistributionTest.ResultPack.Info attribute) (ProportionBasedTest.ResultPack.Info attribute)

NOT_ALIGNED (TagSupportingReads.SupportFlags attribute) NOT_ALT (TagSupportingReads.SupportFlags attribute) nsamples_threshold (FixedParamsDVF attribute) (FixedParamsLQF attribute)

O

ON_THRESHOLD (AlignmentScoreTest.ResultPack.Info attribute) ONE_STRAND_DISTRIB (AnomalousDistributionTest.ResultPack.Info attribute) outcome (AlignmentScoreTest.ResultPack attribute) (AnomalousDistributionTest.ResultPack attribute) (ProportionBasedTest.ResultPack attribute) (ResultPackProtocol attribute)

OVERLAP_TAG (Tags attribute)

P

POOR_ALIGNMENT_SCORE (FlaggerNamespaces attribute) prime() (ReadAwareProcess method) ProcessEngineProtocol (class in hairpin2.infrastructure.process_engines) ProcessError ProcessKindEnum (class in hairpin2.infrastructure.process_engines) ProcessNamespace (FlaggerADF attribute) (FlaggerALF attribute) (FlaggerDVF attribute) (FlaggerLQF attribute) (ReadAwareProcess attribute) (ReadAwareProcessProtocol attribute) (TaggerDupmark attribute) (TaggerLowQual attribute) (TaggerOverlap attribute) (TaggerSupporting attribute)

ProcessType (FlaggerADF attribute) (FlaggerALF attribute) (FlaggerDVF attribute) (FlaggerLQF attribute) (ReadAwareProcess attribute) (ReadAwareProcessProtocol attribute) (TaggerDupmark attribute) (TaggerLowQual attribute) (TaggerOverlap attribute) (TaggerSupporting attribute) prop_loss (ProportionBasedTest.ResultPack attribute) ProportionBasedTest (class in hairpin2.sci_funcs) ProportionBasedTest.ResultPack (class in hairpin2.sci_funcs) ProportionBasedTest.ResultPack.Info (class in hairpin2.sci_funcs)

Q

QualParams (class in hairpin2.process_wrappers.LQF)

R

R (Strand attribute) RAExec (class in hairpin2.infrastructure.rascheduler) read (TagStutterDuplicateReads.FragmentEndpoints attribute) read_has_mark() (in module hairpin2.infrastructure.structures) read_loss_threshold (FixedParamsDVF attribute) (FixedParamsLQF attribute) ReadAwareProcess (class in hairpin2.infrastructure.process) ReadAwareProcessProtocol (class in hairpin2.infrastructure.process) reads (RunParams attribute) reads_seen (FlagResult attribute) (ResultADF attribute) (ResultALF attribute) (ResultDVF attribute) ReadTaggerEngine (class in hairpin2.infrastructure.process_engines) ReadView (class in hairpin2.infrastructure.structures) reason (AlignmentScoreTest.ResultPack attribute) (AnomalousDistributionTest.ResultPack attribute) (ProportionBasedTest.ResultPack attribute) (ResultPackProtocol attribute) record (RunParams attribute)

record_operation() (in module hairpin2.infrastructure.structures) require_marks (ReadAwareProcess property) (ReadAwareProcessProtocol property) require_properties_check() (ReadAwareProcess method) reset() (ReadAwareProcess method) (ReadAwareProcessProtocol method) ResultADF (class in hairpin2.process_wrappers.ADF) ResultALF (class in hairpin2.process_wrappers.ALF) ResultDVF (class in hairpin2.process_wrappers.DVF) ResultLQF (class in hairpin2.process_wrappers.LQF) ResultPack (VariantTestProtocol attribute) ResultPackProtocol (class in hairpin2.infrastructure.structures) run() (RAExec method) run_params (ReadAwareProcess property) (ReadAwareProcessProtocol property) run_process() (ProcessEngineProtocol method) (ReadTaggerEngine method) (VariantFlaggerEngine method) RunParams (class in hairpin2.infrastructure.process_params) RunParamsShared (class in hairpin2.process_wrappers.shared)

S

SAMFLAG (TagSupportingReads.SupportFlags attribute) SHORT (TagSupportingReads.SupportFlags attribute) strand (AnomalousDistributionTest.ResultPack attribute) Strand (class in hairpin2.const)

strand (ResultADF attribute) STUTTER_DUP_TAG (Tags attribute) SUB (MutTypes attribute) SUPPORT_TAG (Tags attribute)

T

tag_dups() (in module hairpin2.process_wrappers.DVF) tag_lq() (in module hairpin2.process_wrappers.LQF) tag_overlap() (in module hairpin2.process_wrappers.mark_overlap) tag_supporting() (in module hairpin2.process_wrappers.mark_support) TagFragmentReads (class in hairpin2.sci_funcs) TAGGER (ProcessKindEnum attribute) tagger_params (ReadTaggerEngine property) TaggerDupmark (class in hairpin2.process_wrappers.DVF) TaggerLowQual (class in hairpin2.process_wrappers.LQF) TaggerNamespaces (class in hairpin2.const) TaggerOverlap (class in hairpin2.process_wrappers.mark_overlap) taggers (RAExec property) TaggerSupporting (class in hairpin2.process_wrappers.mark_support) TagLowQualReads (class in hairpin2.sci_funcs) TagLowQualReads.QualFlags (class in hairpin2.sci_funcs)

Tags (class in hairpin2.const) TagStutterDuplicateReads (class in hairpin2.sci_funcs) TagStutterDuplicateReads.FragmentEndpoints (class in hairpin2.sci_funcs) TagSupportingReads (class in hairpin2.sci_funcs) TagSupportingReads.SupportFlags (class in hairpin2.sci_funcs) test_adf() (in module hairpin2.process_wrappers.ADF) test_ALF() (in module hairpin2.process_wrappers.ALF) test_DVF() (in module hairpin2.process_wrappers.DVF) test_variant_LQF() (in module hairpin2.process_wrappers.LQF) test_variant_reads() (AlignmentScoreTest class method) (AnomalousDistributionTest class method) (ProportionBasedTest class method) (VariantTestProtocol class method) TestOutcomes (class in hairpin2.infrastructure.structures) THRESHOLD (ProportionBasedTest.ResultPack.Info attribute)

U

unwrapped (DataExtensionBase property)

V

validate_exec() (RAExec static method) validate_flagger_exec() (RAExec static method) validate_positive() (in module hairpin2.process_wrappers.ADF) validate_read_map() (ReadView static method) validate_tagger_order() (RAExec static method) ValidNucleotides (class in hairpin2.const)

values() (ReadView method) VARIANT_FAIL (TestOutcomes attribute) variant_flagged (FlagResult attribute) VARIANT_PASS (TestOutcomes attribute) VariantFlaggerEngine (class in hairpin2.infrastructure.process_engines) VariantTestProtocol (class in hairpin2.infrastructure.structures)