Module Expr Str ImportFrom alias ImportFrom alias ImportFrom alias Import alias Import alias Import alias identifier Import alias identifier ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad decorator_list decorator_list ClassDef bases NameLoad body Expr Str decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad body Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad If AttributeLoad NameLoad attr body Assign NameStore Str orelse Assign NameStore Str Assign NameStore Str If CompareIsNot AttributeLoad NameLoad attr NameLoad body Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad keyword NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr ListLoad AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr For NameStore NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Str Dict Str Str ListLoad Dict Str Str AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad AttributeLoad NameLoad attr attr Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Num If CompareIn Str NameLoad body Assign NameStore SubscriptLoad NameLoad Index Str For NameStore NameLoad body Assign NameStore SubscriptLoad NameLoad Index Str Assign SubscriptStore NameLoad Index NameLoad NameLoad AugAssignAdd NameStore Num Return NameLoad decorator_list decorator_list ClassDef bases NameLoad body Expr Str Assign NameStore Str Assign NameStore Call NameLoad ListLoad Str Str Str Assign NameStore Call NameLoad ListLoad Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Assign NameStore Call NameLoad ListLoad Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Assign NameStore Call NameLoad ListLoad Str FunctionDef arguments args NameParam defaults body Raise Call NameLoad Str decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr NameLoad If CompareIsNot AttributeLoad NameLoad attr NameLoad body Assign NameStore AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index NameLoad If CompareIs AttributeLoad NameLoad attr NameLoad body Assign AttributeStore NameLoad attr Num orelse Assign AttributeStore NameLoad attr Call NameLoad AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr If CompareIsNot AttributeLoad NameLoad attr NameLoad body Assign AttributeStore NameLoad attr AttributeLoad AttributeLoad NameLoad attr attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr NameLoad If CompareIs AttributeLoad NameLoad attr NameLoad body Assign AttributeStore NameLoad attr Num orelse Assign NameStore AttributeLoad AttributeLoad NameLoad attr attr Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index NameLoad If CompareIs AttributeLoad NameLoad attr NameLoad body Assign AttributeStore NameLoad attr Num orelse Assign AttributeStore NameLoad attr Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr NameLoad Return NameLoad decorator_list NameLoad FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Num If CompareEq AttributeLoad NameLoad attr Num body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr If UnaryOpNot AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr If CompareIs AttributeLoad NameLoad attr NameLoad body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr If CompareIs AttributeLoad NameLoad attr NameLoad body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr If BoolOpAnd CompareIsNot AttributeLoad NameLoad attr NameLoad CompareEq AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr AttributeLoad AttributeLoad NameLoad attr attr body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr If BoolOpAnd CompareIsNot AttributeLoad NameLoad attr NameLoad CompareEq AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad AttributeLoad NameLoad attr attr body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr If CompareIs AttributeLoad NameLoad attr NameLoad body Pass orelse If CompareEq AttributeLoad NameLoad attr Num body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr orelse If CompareEq AttributeLoad NameLoad attr Num body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr orelse Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr If AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr If AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr If AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr If AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr Return NameLoad decorator_list NameLoad FunctionDef arguments args NameParam NameParam defaults body Assign NameStore ListLoad If CompareIsNot AttributeLoad NameLoad attr NameLoad body For NameStore AttributeLoad AttributeLoad NameLoad attr attr body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Assign NameStore Call NameLoad AttributeLoad NameLoad attr Assign NameStore TupleLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Return Call NameLoad NameLoad decorator_list NameLoad FunctionDef arguments args NameParam NameParam NameParam defaults body If CompareIn SubscriptLoad NameLoad Index Num AttributeLoad NameLoad attr body Return Call AttributeLoad SubscriptLoad NameLoad Index Num attr AttributeLoad NameLoad attr orelse If CompareIn NameLoad AttributeLoad NameLoad attr body Return Call NameLoad SubscriptLoad NameLoad Index Num orelse If CompareIn NameLoad AttributeLoad NameLoad attr body Return Call AttributeLoad SubscriptLoad NameLoad Index Num attr AttributeLoad NameLoad attr orelse If CompareIn NameLoad AttributeLoad NameLoad attr body Return ListComp Call NameLoad NameLoad comprehension NameStore NameLoad orelse Raise Call NameLoad Call AttributeLoad Str attr NameLoad decorator_list NameLoad FunctionDef arguments args NameParam NameParam defaults body Assign NameStore ListLoad For TupleStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr body Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr TupleLoad Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad Assign NameStore Call NameLoad NameLoad Return NameLoad decorator_list NameLoad decorator_list ClassDef bases NameLoad body Pass decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam defaults body Assign NameStore AttributeLoad NameLoad attr Expr Call NameLoad Str AttributeLoad NameLoad attr Expr Call NameLoad Str AttributeLoad NameLoad attr Expr Call NameLoad Str For NameStore AttributeLoad NameLoad attr body Expr Call NameLoad Str NameLoad decorator_list FunctionDef arguments args NameParam defaults body For NameStore AttributeLoad NameLoad attr body Expr Call NameLoad NameLoad Break decorator_list FunctionDef arguments args NameParam defaults body Expr Str Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr decorator_list decorator_list
N/A N/A 
Provides classes that take protocol requests, send that request to
the server, and write a particular genomics file type with the results.
 __future__ division __future__ print_function __future__ unicode_literals N/A collections N/A pysam N/A ga4gh.datamodel.reads reads N/A ga4gh.protocol protocol AbstractConverter N/A object N/A N/A 
    Abstract base class for converter classes
     __init__ N/A N/A self container objectIterator outputFile binaryOutput N/A N/A N/A N/A self _container container N/A N/A self _objectIterator objectIterator N/A N/A self _outputFile outputFile N/A N/A self _binaryOutput binaryOutput N/A N/A SamException N/A Exception N/A N/A 
    Something that went wrong during converting a SAM file
     N/A SamConverter N/A object N/A N/A 
    Converts a requested range from a GA4GH server into a SAM file.
     __init__ N/A N/A self client readGroupId referenceId start end outputFileName binaryOutput N/A None None None None None False N/A N/A N/A self _client client N/A N/A self _readGroup N/A N/A N/A self _client getReadGroup readGroupId N/A N/A self _reference N/A N/A N/A self _client getReference referenceId N/A N/A self _start start N/A N/A self _end end N/A N/A self _outputFileName outputFileName N/A N/A self _binaryOutput binaryOutput N/A convert N/A N/A self N/A N/A N/A header N/A N/A self _getHeader N/A targetIds N/A N/A self _getTargetIds header N/A N/A self _binaryOutput N/A N/A flags wb N/A N/A flags wh N/A fileString - N/A N/A N/A self _outputFileName None N/A N/A fileString N/A self _outputFileName N/A alignmentFile N/A N/A pysam AlignmentFile fileString flags header header N/A iterator N/A N/A N/A self _client searchReads N/A N/A N/A self _readGroup id N/A N/A self _reference id N/A self _start N/A self _end N/A read iterator N/A N/A alignedSegment N/A N/A SamLine toAlignedSegment read targetIds N/A N/A N/A alignmentFile write alignedSegment N/A N/A N/A alignmentFile close N/A _getHeader N/A N/A self N/A N/A N/A header N/A HD SQ N/A VN 1.0 N/A N/A LN SN N/A N/A self _reference length N/A N/A self _reference name N/A header N/A _getTargetIds N/A N/A self header N/A N/A N/A targetIds N/A N/A collections defaultdict int N/A targetId 0 N/A N/A SQ header N/A N/A headerLines N/A header N/A SQ N/A headerLine headerLines N/A N/A refName N/A headerLine N/A SN N/A N/A targetIds N/A refName targetId N/A targetId 1 N/A targetIds N/A N/A SamLine N/A object N/A N/A 
    Methods for processing a line in a SAM file
     N/A _encoding utf8 N/A _tagReservedFieldPrefixes N/A set N/A X Y Z N/A _tagIntegerFields N/A set N/A AM AS CM CP FI H0 H1 H2 HI IH MQ NH NM OP PQ SM TC UQ N/A _tagStringFields N/A set N/A BC BQ CC CO CQ CS CT E2 FS LB MC MD OQ OC PG PT PU QT Q2 R2 RG RT SA U2 N/A _tagIntegerArrayFields N/A set N/A FZ __init__ N/A N/A self N/A N/A N/A N/A SamException SamLine can't be instantiated N/A toAlignedSegment N/A N/A cls read targetIds N/A N/A N/A ret N/A N/A pysam AlignedSegment N/A N/A ret query_name N/A N/A N/A read fragmentName encode N/A cls _encoding N/A N/A ret query_sequence N/A N/A N/A read alignedSequence encode N/A cls _encoding N/A N/A ret flag N/A N/A cls toSamFlag read N/A N/A N/A read alignment None N/A N/A refName N/A N/A N/A read alignment position referenceName N/A N/A ret reference_id N/A targetIds N/A refName N/A N/A N/A read alignment None N/A N/A N/A ret reference_start 0 N/A N/A N/A ret reference_start N/A int N/A N/A N/A read alignment position position N/A N/A N/A read alignment None N/A N/A N/A ret mapping_quality N/A N/A read alignment mappingQuality N/A N/A ret cigar N/A N/A cls toCigar read N/A N/A N/A read nextMatePosition None N/A N/A N/A ret next_reference_id -1 N/A N/A nextRefName N/A N/A read nextMatePosition referenceName N/A N/A ret next_reference_id N/A targetIds N/A nextRefName N/A N/A N/A read nextMatePosition None N/A N/A N/A ret next_reference_start -1 N/A N/A N/A ret next_reference_start N/A int N/A N/A read nextMatePosition position N/A N/A ret template_length N/A read fragmentLength N/A N/A ret query_qualities N/A read alignedQuality N/A N/A ret tags N/A N/A cls toTags read N/A ret N/A classmethod toSamFlag N/A N/A cls read N/A N/A N/A flag 0 N/A N/A N/A read numberReads 2 N/A N/A flag N/A N/A N/A reads SamFlags setFlag flag N/A N/A reads SamFlags READ_PAIRED N/A N/A N/A read improperPlacement N/A N/A flag N/A N/A N/A reads SamFlags setFlag flag N/A N/A reads SamFlags READ_PROPER_PAIR N/A N/A N/A read alignment None N/A N/A flag N/A N/A N/A reads SamFlags setFlag flag N/A N/A reads SamFlags READ_UNMAPPED N/A N/A N/A read nextMatePosition None N/A N/A flag N/A N/A N/A reads SamFlags setFlag flag N/A N/A reads SamFlags MATE_UNMAPPED N/A N/A N/A N/A read alignment None N/A N/A N/A N/A read alignment position strand N/A N/A protocol Strand NEG_STRAND N/A N/A flag N/A N/A N/A reads SamFlags setFlag flag N/A N/A reads SamFlags READ_REVERSE_STRAND N/A N/A N/A N/A read nextMatePosition None N/A N/A N/A read nextMatePosition strand N/A N/A protocol Strand NEG_STRAND N/A N/A flag N/A N/A N/A reads SamFlags setFlag flag N/A N/A reads SamFlags MATE_REVERSE_STRAND N/A N/A N/A read readNumber None N/A N/A N/A N/A N/A N/A read readNumber 0 N/A N/A flag N/A N/A N/A reads SamFlags setFlag flag N/A N/A reads SamFlags FIRST_IN_PAIR N/A N/A N/A N/A read readNumber 1 N/A N/A flag N/A N/A N/A reads SamFlags setFlag flag N/A N/A reads SamFlags SECOND_IN_PAIR N/A N/A flag N/A N/A N/A reads SamFlags setFlag flag N/A N/A reads SamFlags FIRST_IN_PAIR N/A flag N/A N/A N/A reads SamFlags setFlag flag N/A N/A reads SamFlags SECOND_IN_PAIR N/A N/A read secondaryAlignment N/A N/A flag N/A N/A N/A reads SamFlags setFlag flag N/A N/A reads SamFlags SECONDARY_ALIGNMENT N/A N/A read failedVendorQualityChecks N/A N/A flag N/A N/A N/A reads SamFlags setFlag flag N/A N/A reads SamFlags FAILED_QUALITY_CHECK N/A N/A read duplicateFragment N/A N/A flag N/A N/A N/A reads SamFlags setFlag flag N/A N/A reads SamFlags DUPLICATE_READ N/A N/A read supplementaryAlignment N/A N/A flag N/A N/A N/A reads SamFlags setFlag flag N/A N/A reads SamFlags SUPPLEMENTARY_ALIGNMENT N/A flag N/A classmethod toCigar N/A N/A cls read N/A N/A N/A cigarTuples N/A N/A N/A N/A read alignment None N/A N/A gaCigarUnit N/A N/A read alignment cigar N/A N/A operation N/A N/A N/A reads SamCigar ga2int N/A gaCigarUnit operation N/A length N/A int N/A gaCigarUnit operationLength N/A cigarTuple N/A operation length N/A N/A N/A cigarTuples append cigarTuple N/A N/A tuple cigarTuples N/A classmethod _parseTagValue N/A N/A cls tag value N/A N/A N/A N/A N/A tag N/A 0 N/A cls _tagReservedFieldPrefixes N/A N/A N/A N/A N/A value N/A 0 encode N/A cls _encoding N/A N/A N/A tag N/A cls _tagIntegerFields N/A N/A N/A int N/A value N/A 0 N/A N/A N/A tag N/A cls _tagStringFields N/A N/A N/A N/A N/A value N/A 0 encode N/A cls _encoding N/A N/A N/A tag N/A cls _tagIntegerArrayFields N/A N/A N/A N/A int integerString N/A integerString value N/A N/A N/A SamException N/A N/A unrecognized tag '{}' format tag N/A classmethod toTags N/A N/A cls read N/A N/A N/A tags N/A N/A N/A tag value N/A N/A N/A read info items N/A N/A val N/A N/A cls _parseTagValue tag value N/A N/A N/A tags append N/A N/A N/A tag encode N/A cls _encoding val N/A retval N/A tuple tags N/A retval N/A classmethod N/A VcfException N/A Exception N/A N/A N/A VcfConverter N/A AbstractConverter N/A N/A 
    Converts the Variants represented by a SearchVariantsRequest into
    VCF format using pysam.
     _writeHeader N/A N/A self N/A N/A N/A variantSet N/A self _container N/A N/A print ID =  N/A variantSet id N/A N/A print Dataset ID =  N/A variantSet datasetId N/A N/A print Metadata =  N/A metadata N/A variantSet metadata N/A N/A N/A print metadata N/A _writeBody N/A N/A self N/A N/A N/A variant N/A self _objectIterator N/A N/A N/A print variant N/A N/A convert N/A N/A self N/A N/A N/A 
        Run the conversion process.
         N/A N/A N/A self _writeHeader N/A N/A N/A self _writeBody N/A N/A