Module Import alias alias alias alias alias alias alias Import alias ImportFrom alias alias ImportFrom alias ImportFrom alias Assign NameStore Call AttributeLoad NameLoad attr keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str FunctionDef arguments args defaults kwarg body If CompareEq Call NameLoad NameLoad Num body Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Slice Num TryExcept body Assign TupleStore NameStore NameStore NameStore Call NameLoad SubscriptLoad NameLoad Index Str keyword Str handlers ExceptHandler type NameLoad name NameStore body Expr Call AttributeLoad NameLoad attr Num BinOpAdd Call NameLoad Call NameLoad NameLoad Str If CompareIs NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr Num BinOpAdd Call NameLoad BinOpAdd BinOpAdd Str SubscriptLoad NameLoad Index Str Str Str Assign NameStore SubscriptLoad NameLoad Index Str If CompareIs NameLoad NameLoad body Assign NameStore BinOpAdd Call AttributeLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str attr Str Str Str If CompareEq SubscriptLoad NameLoad Index Str Str body Assign NameStore AttributeLoad NameLoad attr orelse Assign NameStore Call NameLoad NameLoad Str Assign NameStore SubscriptLoad NameLoad Index Str Assign NameStore SubscriptLoad NameLoad Index Str Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index Str TryExcept body Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Index Str handlers ExceptHandler body Raise Call AttributeLoad NameLoad attr Str Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad attr If CompareIsNot SubscriptLoad NameLoad Index Str NameLoad body Assign NameStore SubscriptLoad NameLoad Index Str If UnaryOpNot Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Raise Call AttributeLoad NameLoad attr Str orelse Assign NameStore AttributeLoad Call AttributeLoad NameLoad attr keyword Str keyword Str keyword NameLoad attr Expr Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad NameLoad Index Str Index Str NameLoad If SubscriptLoad NameLoad Index Str body Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr attr Str Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr attr Str Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr attr Str Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr attr Str Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr attr Str Expr Call AttributeLoad NameLoad attr Str If CompareIsNot NameLoad NameLoad body For TupleStore NameStore NameStore Call AttributeLoad Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr attr body Expr Call AttributeLoad NameLoad attr BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str SubscriptLoad NameLoad Index Str Str SubscriptLoad NameLoad Index Str Str SubscriptLoad NameLoad Index Str Str If CompareGt Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr Str If CompareIsNot NameLoad NameLoad body For TupleStore NameStore NameStore Call AttributeLoad Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr attr body Expr Call AttributeLoad NameLoad attr BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str SubscriptLoad NameLoad Index Str Str SubscriptLoad NameLoad Index Str Str SubscriptLoad NameLoad Index Str Str If CompareIsNot NameLoad NameLoad body For TupleStore NameStore NameStore Call AttributeLoad Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr attr body Expr Call AttributeLoad NameLoad attr BinOpAdd BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str SubscriptLoad NameLoad Index Str Str If CompareIsNot NameLoad NameLoad body For TupleStore NameStore NameStore Call AttributeLoad Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr attr body Expr Call AttributeLoad NameLoad attr BinOpAdd BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str NameLoad Str For NameStore Call NameLoad Call NameLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str body Expr Call AttributeLoad NameLoad attr BinOpAdd BinOpAdd BinOpAdd BinOpAdd Str SubscriptLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str Index NameLoad Str Call NameLoad SubscriptLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str Index NameLoad Str Expr Call AttributeLoad NameLoad attr Str If CompareGt Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr Str For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr BinOpAdd Str NameLoad Expr Call AttributeLoad NameLoad attr Str Assign NameStore Dict For NameStore Call NameLoad Call NameLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str body Assign SubscriptStore NameLoad Index SubscriptLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str Index NameLoad SubscriptLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str Index NameLoad Assign NameStore Call AttributeLoad Call NameLoad NameLoad Str attr Assign NameStore Dict Assign NameStore Call AttributeLoad NameLoad attr For NameStore Call NameLoad Call NameLoad NameLoad body Assign SubscriptStore NameLoad Index SubscriptLoad NameLoad Index NameLoad BinOpAdd NameLoad Num Assign NameStore Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index Str Index Str If CompareIsNot SubscriptLoad NameLoad Index Str NameLoad body Assign NameStore ListLoad For NameStore NameLoad body If CompareIn NameLoad SubscriptLoad NameLoad Index Str body Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore SubscriptLoad NameLoad Slice For NameStore NameLoad body Assign NameStore ListLoad Assign NameStore Num Assign NameStore Call AttributeLoad NameLoad attr keyword NameLoad keyword Num keyword AttributeLoad NameLoad attr For NameStore SubscriptLoad Call AttributeLoad NameLoad attr keyword NameLoad keyword Num Index Str body Assign NameStore SubscriptLoad NameLoad Index Num For NameStore Call AttributeLoad NameLoad attr keyword NameLoad body If CompareNotEq SubscriptLoad NameLoad Index Num NameLoad body Break If CompareLt NameLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str body Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Assign NameStore ListLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Assign NameStore ListLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults body For NameStore NameLoad body Assign NameStore NameLoad Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str attr Str For NameStore NameLoad body If BoolOpAnd BoolOpOr CompareNotEq Call NameLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str Call NameLoad NameLoad CompareEq Call NameLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str Num CompareEq Call NameLoad NameLoad Num UnaryOpNot Call AttributeLoad NameLoad attr Str NameLoad body Assign NameStore NameLoad Break If NameLoad body Expr Call NameLoad SubscriptLoad NameLoad Slice NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad For NameStore NameLoad body Assign NameStore NameLoad Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str attr Str For NameStore NameLoad body If BoolOpAnd BoolOpOr CompareNotEq Call NameLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str Call NameLoad NameLoad CompareEq Call NameLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str Num CompareEq Call NameLoad NameLoad Num UnaryOpNot Call AttributeLoad NameLoad attr Str NameLoad body Assign NameStore NameLoad Break If CompareEq NameLoad NameLoad body Expr Call NameLoad SubscriptLoad NameLoad Slice NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults body If Call NameLoad NameLoad NameLoad Str body If NameLoad body Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad orelse If Call NameLoad NameLoad NameLoad Str body If NameLoad body Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad orelse Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Str NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults body Assign NameStore Call AttributeLoad Call NameLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str attr Assign NameStore BinOpAdd SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str Num Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str attr Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str attr Assign NameStore Str If CompareIsNot Call AttributeLoad NameLoad attr Str NameLoad body If CompareNotEq SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str Str body Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str attr Assign NameStore Str If CompareIsNot Call AttributeLoad NameLoad attr Str NameLoad body If CompareNotEq SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str Str body Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str attr orelse Assign NameStore Str Assign NameStore Str If CompareIsNot Call AttributeLoad NameLoad attr Str NameLoad body If BoolOpOr CompareNotEq SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str AttributeLoad NameLoad attr CompareEq SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str Num body Assign NameStore SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str Assign NameStore Num Assign NameStore NameLoad Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str attr Str If CompareEq NameLoad ListLoad Str body Assign NameStore NameLoad For NameStore NameLoad body If BoolOpAnd BoolOpOr CompareNotEq Call NameLoad NameLoad Call NameLoad NameLoad CompareEq Call NameLoad NameLoad Num CompareEq Call NameLoad NameLoad Num UnaryOpNot Call AttributeLoad NameLoad attr Str NameLoad body Assign NameStore NameLoad If NameLoad body Assign NameStore BinOpAdd SubscriptLoad NameLoad Index BinOpSub BinOpAdd SubscriptLoad NameLoad Index NameLoad Call NameLoad NameLoad Num NameLoad Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index Str attr Str Assign NameStore Str For NameStore NameLoad body If Call AttributeLoad NameLoad attr Str NameLoad body AugAssignAdd NameStore BinOpAdd NameLoad Str orelse AugAssignAdd NameStore BinOpAdd BinOpAdd SubscriptLoad NameLoad Index BinOpSub BinOpAdd SubscriptLoad NameLoad Index NameLoad Call NameLoad NameLoad Num NameLoad Str Assign NameStore NameLoad Assign NameStore Call AttributeLoad NameLoad attr Str AugAssignSub NameStore Num Expr Call AttributeLoad NameLoad attr BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd NameLoad Str Call AttributeLoad Call NameLoad NameLoad attr Str Call AttributeLoad Call NameLoad NameLoad attr Str Call AttributeLoad Call AttributeLoad NameLoad attr attr Str Call AttributeLoad Call AttributeLoad NameLoad attr attr Str Call AttributeLoad Call NameLoad NameLoad attr Str Call AttributeLoad Call NameLoad NameLoad attr Assign NameStore Str For NameStore NameLoad body If CompareIn Str NameLoad body If CompareIsNot Call AttributeLoad NameLoad attr NameLoad NameLoad body If Call NameLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index NameLoad NameLoad body If CompareEq SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index NameLoad NameLoad body AugAssignAdd NameStore BinOpAdd Call AttributeLoad NameLoad attr Str Str orelse If Call NameLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index NameLoad body AugAssignAdd NameStore BinOpAdd BinOpAdd BinOpAdd Call AttributeLoad NameLoad attr Str Str Call NameLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index NameLoad Str If CompareEq NameLoad Str body Assign NameStore Str Expr Call AttributeLoad NameLoad attr BinOpAdd Str Call AttributeLoad NameLoad attr Str Assign NameStore Num Assign NameStore NameLoad Assign NameStore NameLoad While Num body If CompareIs Call AttributeLoad NameLoad attr BinOpAdd Str Call NameLoad NameLoad NameLoad body Break If CompareEq NameLoad NameLoad body Assign NameStore Call AttributeLoad NameLoad attr BinOpAdd Str Call NameLoad NameLoad If CompareEq NameLoad NameLoad body Assign NameStore Call AttributeLoad NameLoad attr BinOpAdd Str Call NameLoad NameLoad AugAssignAdd NameStore Num Assign NameStore ListLoad For NameStore NameLoad body If CompareIn Str NameLoad body If CompareIsNot Call AttributeLoad NameLoad attr NameLoad NameLoad body Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Slice Num Expr Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad Str attr NameLoad If CompareNotIn NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad If CompareIsNot Call AttributeLoad NameLoad attr Str NameLoad body Expr Call AttributeLoad NameLoad attr Str Assign NameStore Str If NameLoad body AugAssignAdd NameStore Str If NameLoad body AugAssignAdd NameStore Str For NameStore NameLoad body AugAssignAdd NameStore BinOpAdd NameLoad Str Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Str Assign NameStore Num While Num body If CompareIsNot Call AttributeLoad NameLoad attr BinOpAdd Str Call NameLoad NameLoad NameLoad body Assign NameStore BinOpAdd SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index BinOpAdd Str Call NameLoad NameLoad Str If NameLoad body If Call AttributeLoad NameLoad attr BinOpAdd Str Call NameLoad NameLoad body Assign NameStore SubscriptLoad NameLoad Index Call AttributeLoad NameLoad attr BinOpAdd Str Call NameLoad NameLoad AugAssignAdd NameStore BinOpAdd NameLoad Str orelse AugAssignAdd NameStore Str If NameLoad body If CompareIsNot Call AttributeLoad NameLoad attr BinOpAdd Str Call NameLoad NameLoad NameLoad body Assign NameStore SubscriptLoad NameLoad Index Call AttributeLoad NameLoad attr BinOpAdd Str Call NameLoad NameLoad If BoolOpOr CompareEq NameLoad AttributeLoad NameLoad attr CompareEq NameLoad Num body AugAssignAdd NameStore Str orelse AugAssignAdd NameStore BinOpAdd Call NameLoad NameLoad Str orelse AugAssignAdd NameStore Str For NameStore NameLoad body If CompareIsNot Call AttributeLoad NameLoad attr BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str Call NameLoad NameLoad NameLoad body If Call NameLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str Call NameLoad NameLoad NameLoad body If SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str Call NameLoad NameLoad body AugAssignAdd NameStore NameLoad orelse AugAssignAdd NameStore Str orelse If BoolOpOr CompareEq SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str Call NameLoad NameLoad AttributeLoad NameLoad attr CompareEq SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str Call NameLoad NameLoad Num body AugAssignAdd NameStore Str orelse AugAssignAdd NameStore Call NameLoad SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str Call NameLoad NameLoad orelse AugAssignAdd NameStore Str AugAssignAdd NameStore Str Expr Call AttributeLoad NameLoad attr BinOpAdd Str Call AttributeLoad NameLoad attr Str orelse Break AugAssignAdd NameStore Num Expr Call AttributeLoad NameLoad attr Str decorator_list FunctionDef arguments args NameParam defaults body If Call NameLoad NameLoad NameLoad body If BoolOpOr CompareEq NameLoad AttributeLoad NameLoad attr CompareEq NameLoad Num body Return NameLoad If Call NameLoad NameLoad NameLoad body If CompareEq NameLoad NameLoad body Return NameLoad If Call NameLoad NameLoad NameLoad body If BoolOpOr CompareEq NameLoad AttributeLoad NameLoad attr CompareEq NameLoad Num body Return NameLoad If CompareEq NameLoad Str body Return NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Num While Num body If CompareIs Call AttributeLoad NameLoad attr BinOpAdd Str Call NameLoad NameLoad NameLoad body If CompareGt NameLoad Num body Return NameLoad orelse Return NameLoad If CompareNotEq SubscriptLoad NameLoad Index SubscriptLoad NameLoad Index BinOpAdd Str Call NameLoad NameLoad NameLoad body Return NameLoad AugAssignAdd NameStore Num decorator_list If CompareEq NameLoad Str body Expr Call NameLoad
N/A N/A os sys re math argparse collections tempfile N/A dxpy utils.resolver ResolutionError resolve_existing_path utils.printing fill compat str N/A parser N/A N/A argparse ArgumentParser description Export a Variants gtable into a VCF file.  WARNING: This can take a while because it downloads the entire reference genome.  It is recommended that this script only be called from within an application running on the cloud. N/A N/A N/A parser add_argument path help Path to the Variants gtable N/A N/A N/A parser add_argument -o --output help Name of file to write VCF to ("-" indicates stdout output) N/A N/A N/A parser add_argument --export-ref-calls action store_true help If selected, rows confidently called as non-variants will also be written N/A N/A N/A parser add_argument --export-no-calls action store_true help If selected, rows in which no confident call could be made will also be written N/A N/A N/A parser add_argument --chr action append help If any chr are provided, export will only write rows of the specified chromosomes; repeat to include additional chromosomes N/A N/A N/A parser add_argument --no-write-header dest write_header action store_false help If selected, do not write the header the VCF file (useful for concatenating files together with chr N/A N/A N/A parser add_argument --reference help If present, take reference from this file instead of trying to download it main N/A N/A N/A kwargs N/A N/A N/A N/A len kwargs 0 N/A N/A kwargs N/A vars N/A N/A parser parse_args N/A N/A sys argv N/A 1 N/A N/A N/A N/A project folderpath entity_result N/A resolve_existing_path N/A kwargs N/A path expected entity N/A N/A N/A ResolutionError N/A details N/A N/A N/A N/A parser exit 1 N/A N/A fill N/A str details N/A N/A entity_result None N/A N/A N/A N/A parser exit 1 N/A N/A fill N/A N/A Could not resolve  N/A kwargs N/A path  to a data object N/A filename N/A kwargs N/A output N/A N/A filename None N/A N/A filename N/A N/A N/A N/A N/A entity_result N/A describe N/A name replace / %2F .vcf N/A N/A N/A kwargs N/A output - N/A N/A outputFile N/A sys stdout N/A N/A outputFile N/A open filename w N/A exportRef N/A kwargs N/A export_ref_calls N/A exportNoCall N/A kwargs N/A export_no_calls N/A variantsTable N/A N/A dxpy open_dxgtable N/A entity_result N/A id N/A N/A N/A originalContigSet N/A N/A N/A variantsTable get_details N/A original_contigset N/A N/A N/A N/A N/A N/A dxpy AppError The original reference genome must be attached as a detail N/A contigDetails N/A N/A N/A N/A dxpy DXRecord originalContigSet get_details N/A N/A N/A kwargs N/A reference None N/A N/A refFileName N/A kwargs N/A reference N/A N/A N/A N/A N/A os path isfile refFileName N/A N/A N/A N/A dxpy AppError The reference expected by the variants to vcf script was not a valid file N/A N/A refFileName N/A N/A N/A tempfile NamedTemporaryFile prefix reference_ suffix .txt delete False name N/A N/A N/A dxpy download_dxfile N/A N/A contigDetails N/A flat_sequence_file N/A $dnanexus_link refFileName N/A N/A kwargs N/A write_header N/A N/A infos N/A N/A N/A N/A variantsTable get_details get infos N/A formats N/A N/A N/A N/A variantsTable get_details get formats N/A alts N/A N/A N/A N/A variantsTable get_details get alts N/A filters N/A N/A N/A N/A variantsTable get_details get filters N/A samples N/A N/A N/A N/A variantsTable get_details get samples N/A N/A N/A outputFile write ##fileformat=VCFv4.1
 N/A N/A infos None N/A N/A N/A k v N/A N/A N/A N/A collections OrderedDict N/A sorted N/A N/A infos iteritems iteritems N/A N/A N/A N/A outputFile write N/A N/A N/A N/A N/A N/A N/A N/A ##INFO=<ID= k ,Number= N/A v N/A number ,Type= N/A v N/A type ,Description=" N/A v N/A description ">
 N/A N/A N/A len samples 0 N/A N/A N/A N/A outputFile write ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 N/A N/A N/A outputFile write ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
 N/A N/A N/A outputFile write ##FORMAT=<ID=DP,Number=1,Type=String,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
 N/A N/A formats None N/A N/A N/A k v N/A N/A N/A N/A collections OrderedDict N/A sorted N/A N/A formats iteritems iteritems N/A N/A N/A N/A outputFile write N/A N/A N/A N/A N/A N/A N/A N/A ##FORMAT=<ID= k ,Number= N/A v N/A number ,Type= N/A v N/A type ,Description=" N/A v N/A description ">
 N/A N/A alts None N/A N/A N/A k v N/A N/A N/A N/A collections OrderedDict N/A sorted N/A N/A alts iteritems iteritems N/A N/A N/A N/A outputFile write N/A N/A N/A N/A ##ALT=<ID= k ,Description=" N/A v N/A description ">
 N/A N/A filters None N/A N/A N/A k v N/A N/A N/A N/A collections OrderedDict N/A sorted N/A N/A filters iteritems iteritems N/A N/A N/A N/A outputFile write N/A N/A N/A N/A ##FILTER=<ID= k ,Description=" v ">
 N/A i N/A range N/A len N/A N/A contigDetails N/A contigs N/A names N/A N/A N/A N/A outputFile write N/A N/A N/A N/A ##contig=<ID= N/A N/A N/A contigDetails N/A contigs N/A names N/A i ,length= N/A str N/A N/A N/A contigDetails N/A contigs N/A sizes N/A i >
 N/A N/A N/A outputFile write #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO N/A N/A N/A len samples 0 N/A N/A N/A N/A outputFile write 	FORMAT N/A x samples N/A N/A N/A N/A outputFile write N/A x N/A N/A N/A outputFile write N/A chromosomeOffsets N/A N/A i N/A range N/A len N/A N/A contigDetails N/A contigs N/A names N/A N/A N/A chromosomeOffsets N/A N/A N/A N/A contigDetails N/A contigs N/A names N/A i N/A N/A N/A contigDetails N/A contigs N/A offsets N/A i N/A contigSequence N/A N/A N/A open refFileName r read N/A col N/A N/A names N/A N/A variantsTable get_col_names N/A i N/A range N/A len names N/A N/A N/A col N/A N/A names N/A i N/A i 1 N/A col N/A N/A collections OrderedDict N/A sorted N/A N/A col items N/A chromosomeList N/A N/A contigDetails N/A contigs N/A names N/A N/A N/A kwargs N/A chr None N/A N/A intersection N/A N/A x chromosomeList N/A N/A N/A x N/A kwargs N/A chr N/A N/A N/A N/A intersection append x N/A chromosomeList N/A intersection N/A N/A chromosome chromosomeList N/A N/A buff N/A N/A lastPosition -1 N/A query N/A N/A variantsTable genomic_range_query chr chromosome lo 0 hi N/A sys maxsize N/A row N/A N/A N/A variantsTable get_rows query query limit 1 N/A data N/A N/A startRow N/A row N/A 0 N/A row N/A N/A variantsTable iterate_rows start startRow N/A N/A N/A N/A row N/A 1 chromosome N/A N/A N/A N/A lastPosition N/A row N/A N/A col N/A lo N/A N/A N/A writeBuffer buff col outputFile contigSequence chromosomeOffsets exportRef exportNoCall N/A buff N/A N/A N/A N/A buff append row N/A lastPosition N/A row N/A N/A col N/A lo N/A N/A writeBuffer buff col outputFile contigSequence chromosomeOffsets exportRef exportNoCall N/A buff N/A N/A writeBuffer N/A N/A buff col outputFile contigSequence chromosomeOffsets exportRef exportNoCall N/A N/A N/A x buff N/A N/A printPreceedingCharacter False N/A altOptions N/A N/A N/A x N/A N/A col N/A alt split , N/A y altOptions N/A N/A N/A N/A N/A N/A len N/A x N/A N/A col N/A ref N/A len y N/A N/A len N/A x N/A N/A col N/A ref 0 N/A N/A len y 0 N/A N/A N/A re search [^ATGCNatgcn\.-] y N/A N/A printPreceedingCharacter True N/A N/A printPreceedingCharacter N/A N/A N/A writeRowCheck N/A x N/A col outputFile contigSequence chromosomeOffsets exportRef exportNoCall N/A x buff N/A N/A printPreceedingCharacter False N/A altOptions N/A N/A N/A x N/A N/A col N/A alt split , N/A y altOptions N/A N/A N/A N/A N/A N/A len N/A x N/A N/A col N/A ref N/A len y N/A N/A len N/A x N/A N/A col N/A ref 0 N/A N/A len y 0 N/A N/A N/A re search [^ATGCNatgcn\.-] y N/A N/A printPreceedingCharacter True N/A N/A N/A printPreceedingCharacter False N/A N/A N/A writeRowCheck N/A x N/A col outputFile contigSequence chromosomeOffsets exportRef exportNoCall N/A writeRowCheck N/A N/A row col outputFile contigSequence chromosomeOffsets exportRef exportNoCall N/A N/A N/A N/A checkRowIsAllType row col ref N/A N/A exportRef N/A N/A N/A writeRow row col outputFile contigSequence chromosomeOffsets N/A N/A N/A checkRowIsAllType row col no-call N/A N/A exportNoCall N/A N/A N/A writeRow row col outputFile contigSequence chromosomeOffsets N/A N/A N/A writeRow row col outputFile contigSequence chromosomeOffsets N/A parseRegions N/A N/A input N/A N/A N/A result N/A N/A x input N/A N/A N/A N/A result append N/A N/A re findall (\w+):(\d+)-(\d+) x N/A result N/A writeRow N/A N/A row col outputFile contigSequence chromosomeOffsets N/A N/A N/A chr N/A N/A N/A str N/A row N/A N/A col N/A chr strip N/A pos N/A N/A row N/A N/A col N/A lo 1 N/A ref N/A N/A N/A row N/A N/A col N/A ref strip N/A alt N/A N/A N/A row N/A N/A col N/A alt strip N/A ids . N/A N/A N/A N/A col get ids None N/A N/A N/A N/A row N/A N/A col N/A ids N/A N/A ids N/A N/A N/A row N/A N/A col N/A ids strip N/A filt . N/A N/A N/A N/A col get filter None N/A N/A N/A N/A row N/A N/A col N/A filter N/A N/A filt N/A N/A N/A row N/A N/A col N/A filter strip N/A N/A filt PASS N/A qual . N/A N/A N/A N/A col get qual None N/A N/A N/A N/A N/A row N/A N/A col N/A qual N/A dxpy NULL N/A N/A row N/A N/A col N/A qual -999999 N/A N/A qual N/A row N/A N/A col N/A qual N/A sample 0 N/A printPreceedingCharacter False N/A altOptions N/A N/A N/A row N/A N/A col N/A alt split , N/A N/A altOptions N/A N/A N/A printPreceedingCharacter True N/A x altOptions N/A N/A N/A N/A N/A N/A len ref N/A len x N/A N/A len ref 0 N/A N/A len alt 0 N/A N/A N/A re search [^ATGCNatgcn\.-] x N/A N/A printPreceedingCharacter True N/A printPreceedingCharacter N/A N/A ref N/A N/A contigSequence N/A N/A N/A N/A chromosomeOffsets N/A chr N/A int pos 2 ref N/A altOptions N/A N/A N/A row N/A N/A col N/A alt split , N/A alt N/A x altOptions N/A N/A N/A N/A re search [^ATGCNatgcn\.-] x N/A N/A alt N/A x , N/A N/A alt N/A N/A N/A contigSequence N/A N/A N/A N/A chromosomeOffsets N/A chr N/A int pos 2 x , N/A validAlt False N/A alt N/A N/A alt rstrip , N/A pos 1 N/A N/A N/A outputFile write N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A chr N/A N/A N/A str pos strip N/A N/A N/A str ids strip N/A N/A N/A N/A ref upper strip N/A N/A N/A N/A alt upper strip N/A N/A N/A str qual strip N/A N/A N/A str filt strip N/A infos N/A x col N/A N/A N/A info_ x N/A N/A N/A N/A N/A col get x None N/A N/A N/A isinstance N/A row N/A N/A col N/A x bool N/A N/A N/A N/A row N/A N/A col N/A x True N/A N/A infos N/A N/A N/A x lstrip info_ ; N/A N/A N/A isDefault N/A row N/A N/A col N/A x N/A N/A infos N/A N/A N/A N/A N/A x lstrip info_ = N/A str N/A row N/A N/A col N/A x ; N/A N/A infos N/A N/A infos . N/A N/A N/A outputFile write N/A N/A N/A infos rstrip ; N/A sample 0 N/A coverage False N/A totalCoverage False N/A 1 N/A N/A N/A N/A N/A col get N/A type_ N/A str sample None N/A N/A N/A N/A coverage False N/A N/A coverage N/A N/A col get N/A coverage_ N/A str sample N/A N/A totalCoverage False N/A N/A totalCoverage N/A N/A col get N/A total_coverage_ N/A str sample N/A sample 1 N/A observedFormats N/A N/A x col N/A N/A N/A format_ x N/A N/A N/A N/A N/A col get x None N/A N/A entrySplit N/A N/A N/A x split _ N/A 1 N/A N/A N/A entrySplit pop N/A tag N/A N/A _ join entrySplit N/A N/A tag observedFormats N/A N/A N/A N/A observedFormats append tag N/A N/A N/A N/A col get type_0 None N/A N/A N/A N/A outputFile write N/A formatOrdering GT: N/A coverage N/A N/A formatOrdering AD: N/A totalCoverage N/A N/A formatOrdering DP: N/A x observedFormats N/A N/A formatOrdering N/A x : N/A N/A N/A outputFile write N/A N/A formatOrdering rstrip : N/A sample 0 N/A 1 N/A N/A N/A N/A N/A col get N/A type_ N/A str sample None N/A N/A formats N/A N/A row N/A N/A col N/A N/A genotype_ N/A str sample : N/A coverage N/A N/A N/A N/A col get N/A coverage_ N/A str sample N/A N/A cov N/A row N/A N/A N/A col get N/A coverage_ N/A str sample N/A formats N/A cov : N/A N/A cov .: N/A totalCoverage N/A N/A N/A N/A N/A col get N/A total_coverage_ N/A str sample None N/A N/A tCov N/A row N/A N/A N/A col get N/A total_coverage_ N/A str sample N/A N/A N/A tCov N/A dxpy NULL N/A tCov -999999 N/A N/A formats 0: N/A N/A formats N/A N/A str tCov : N/A N/A formats .: N/A x observedFormats N/A N/A N/A N/A N/A col get N/A N/A N/A format_ x _ N/A str sample None N/A N/A N/A isinstance N/A row N/A N/A col N/A N/A N/A N/A format_ x _ N/A str sample bool N/A N/A N/A row N/A N/A col N/A N/A N/A N/A format_ x _ N/A str sample N/A N/A formats x N/A N/A formats . N/A N/A N/A N/A N/A row N/A N/A col N/A N/A N/A N/A format_ x _ N/A str sample N/A dxpy NULL N/A N/A row N/A N/A col N/A N/A N/A N/A format_ x _ N/A str sample -999999 N/A N/A formats . N/A N/A formats N/A str N/A row N/A N/A col N/A N/A N/A N/A format_ x _ N/A str sample N/A N/A formats . N/A formats : N/A N/A N/A outputFile write N/A N/A N/A formats rstrip : N/A N/A N/A sample 1 N/A N/A N/A outputFile write N/A isDefault N/A N/A entry N/A N/A N/A N/A isinstance entry float N/A N/A N/A N/A entry N/A dxpy NULL N/A entry -999999 N/A N/A False N/A N/A isinstance entry bool N/A N/A N/A entry False N/A N/A False N/A N/A isinstance entry int N/A N/A N/A N/A entry N/A dxpy NULL N/A entry -999999 N/A N/A False N/A N/A entry N/A N/A False N/A True N/A checkRowIsAllType N/A N/A row col typ N/A N/A N/A sample 0 N/A 1 N/A N/A N/A N/A N/A col get N/A type_ N/A str sample None N/A N/A N/A sample 0 N/A N/A True N/A N/A False N/A N/A N/A row N/A N/A col N/A N/A type_ N/A str sample typ N/A N/A False N/A sample 1 N/A N/A N/A __name__ __main__ N/A N/A N/A main