Module Expr Str ImportFrom alias ImportFrom alias ImportFrom alias Import alias Import alias identifier Import alias identifier ClassDef bases AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Expr Str FunctionDef arguments args NameParam defaults body With Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Num Str Assign NameStore Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore BinOpMult Str BinOpAdd AttributeLoad NameLoad attr Num Assign NameStore Call AttributeLoad NameLoad attr NameLoad Str Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Slice AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body With Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Str Num Num Num Assign NameStore Num Assign NameStore Call AttributeLoad NameLoad attr Num NameLoad Num Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore Num Assign NameStore Call AttributeLoad NameLoad attr Num Num NameLoad Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore Num Assign NameStore Call AttributeLoad NameLoad attr NameLoad Num Num Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body With Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Num Num Str Str Expr Call AttributeLoad NameLoad attr Num Num Str Str decorator_list FunctionDef arguments args NameParam defaults body With Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Num Num Num Str With Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Num Num Num Str Expr Call AttributeLoad NameLoad attr Num Num Num Str decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad NameLoad attr Num Str With Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Str Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore BinOpMult Str BinOpAdd AttributeLoad NameLoad attr Num Assign NameStore BinOpSub AttributeLoad NameLoad attr Num Assign NameStore BinOpAdd AttributeLoad NameLoad attr Num Assign TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Slice AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore BinOpSub AttributeLoad NameLoad attr Num Assign NameStore BinOpAdd AttributeLoad NameLoad attr Num Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr decorator_list decorator_list
N/A N/A 
Tests the pysam sanitizer
 __future__ division __future__ print_function __future__ unicode_literals N/A unittest N/A ga4gh.datamodel datamodel N/A ga4gh.exceptions exceptions TestPysamSanitizer N/A N/A datamodel PysamDatamodelMixin N/A unittest TestCase N/A N/A 
    Test the pysam sanitizer
     testSanitizeString N/A N/A self N/A N/A N/A N/A N/A self assertRaises N/A exceptions DatamodelValidationException N/A N/A N/A N/A self sanitizeString 1 longString N/A shortString shortString N/A N/A N/A self assertIsInstance shortString unicode N/A result N/A N/A self sanitizeString shortString shortString N/A N/A N/A self assertEqual shortString result N/A N/A N/A self assertNotIsInstance result unicode N/A longString N/A x N/A N/A self maxStringLength 1 N/A result N/A N/A self sanitizeString longString longString N/A N/A N/A self assertEqual N/A longString N/A N/A self maxStringLength result N/A testSanitizeInt N/A N/A self N/A N/A N/A N/A N/A self assertRaises N/A exceptions DatamodelValidationException N/A N/A N/A N/A self sanitizeInt whoops 0 0 0 N/A minVal 0 N/A result N/A N/A self sanitizeInt -10 minVal 100 int N/A N/A N/A self assertEqual minVal result N/A maxVal 100 N/A result N/A N/A self sanitizeInt 200 0 maxVal int N/A N/A N/A self assertEqual maxVal result N/A val 50 N/A result N/A N/A self sanitizeInt val 0 100 int N/A N/A N/A self assertEqual result val N/A testAssertValidRange N/A N/A self N/A N/A N/A N/A N/A self assertRaises N/A exceptions DatamodelValidationException N/A N/A N/A N/A self assertValidRange 100 0 start end N/A N/A N/A self assertValidRange 0 100 start end N/A testAssertInRange N/A N/A self N/A N/A N/A N/A N/A self assertRaises N/A exceptions DatamodelValidationException N/A N/A N/A N/A self assertInRange -1 0 100 example N/A N/A N/A self assertRaises N/A exceptions DatamodelValidationException N/A N/A N/A N/A self assertInRange 101 0 100 example N/A N/A N/A self assertInRange 50 0 100 example N/A testAssertInt N/A N/A self N/A N/A N/A N/A N/A self assertInt 5 example N/A N/A N/A self assertRaises N/A exceptions DatamodelValidationException N/A N/A N/A N/A self assertInt 5 example N/A testSanitizeVariantFileFetch N/A N/A self N/A N/A N/A contigArg N/A x N/A N/A self maxStringLength 1 N/A startArg N/A N/A self vcfMin 1 N/A stopArg N/A N/A self vcfMax 1 N/A N/A contig start stop N/A N/A self sanitizeVariantFileFetch contigArg startArg stopArg N/A N/A N/A self assertEqual N/A contigArg N/A N/A self maxStringLength contig N/A N/A N/A self assertEqual start N/A self vcfMin N/A N/A N/A self assertEqual stop N/A self vcfMax N/A testSanitizeAlignmentFileFetch N/A N/A self N/A N/A N/A startArg N/A N/A self samMin 1 N/A endArg N/A N/A self samMaxEnd 1 N/A N/A start end N/A N/A self sanitizeAlignmentFileFetch startArg endArg N/A N/A N/A self assertEqual start N/A self samMin N/A N/A N/A self assertEqual end N/A self samMaxEnd N/A N/A