Module Import alias ImportFrom alias ImportFrom alias ImportFrom alias alias ImportFrom alias alias If UnaryOpNot CompareEq Call NameLoad AttributeLoad NameLoad attr Num body Expr Call AttributeLoad NameLoad attr Str FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore BinOpSub AttributeLoad NameLoad attr AttributeLoad NameLoad attr If CompareLt NameLoad Num body Expr Call AttributeLoad NameLoad attr Str Assign NameStore BinOpMult AttributeLoad NameLoad attr NameLoad If UnaryOpNot CompareGt Call NameLoad BinOpSub AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad body Return NameLoad If BoolOpAnd CompareGtE Call NameLoad BinOpSub AttributeLoad NameLoad attr AttributeLoad NameLoad attr BinOpMult NameLoad NameLoad CompareGt AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Return NameLoad If BoolOpAnd CompareGt Call NameLoad BinOpSub AttributeLoad NameLoad attr AttributeLoad NameLoad attr BinOpMult AttributeLoad NameLoad attr NameLoad CompareGt AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Return NameLoad If BoolOpAnd BoolOpOr CompareEq AttributeLoad NameLoad attr AttributeLoad NameLoad attr CompareEq AttributeLoad NameLoad attr AttributeLoad NameLoad attr BoolOpOr CompareLt AttributeLoad NameLoad attr NameLoad CompareLt AttributeLoad NameLoad attr NameLoad CompareLt BinOpSub AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad CompareLt BinOpSub AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad body Return NameLoad Return NameLoad decorator_list Assign NameStore Call NameLoad Str ListLoad Str Str Assign NameStore Call NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore Call NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore Call NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore Call NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore BinOpAdd Call AttributeLoad NameLoad attr Call AttributeLoad Call AttributeLoad NameLoad attr attr Assign NameStore Dict For NameStore Call NameLoad NameLoad body If UnaryOpNot Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr ListLoad Expr Call AttributeLoad SubscriptLoad NameLoad Index AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad NameLoad attr Assign NameStore Dict For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign TupleStore NameStore NameStore TupleLoad AttributeLoad SubscriptLoad NameLoad Index Num attr Num For NameStore NameLoad body For NameStore AttributeLoad NameLoad attr body Assign NameStore Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr If CompareLt NameLoad NameLoad body Assign NameStore NameLoad Assign NameStore Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr If CompareGt NameLoad NameLoad body Assign NameStore NameLoad Assign SubscriptStore NameLoad Index NameLoad Call NameLoad NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Str Assign NameStore Call NameLoad BinOpAdd NameLoad Str Str Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Str For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign NameStore SubscriptLoad NameLoad Index NameLoad For NameStore NameLoad body Assign NameStore ListLoad For NameStore AttributeLoad NameLoad attr body If Call NameLoad NameLoad NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad orelse Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr BinOpAdd Call NameLoad NameLoad Str Expr Call AttributeLoad NameLoad attr BinOpAdd Call NameLoad NameLoad Str If CompareGt Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr BinOpAdd Call NameLoad NameLoad Str For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr BinOpAdd Call NameLoad NameLoad Str Assign SubscriptStore AttributeLoad NameLoad attr Slice ListLoad For NameStore NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad If CompareGt Call NameLoad AttributeLoad NameLoad attr Num body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr
N/A N/A sys collections namedtuple math fabs nucio getDeltaAlignmentIterator deltaRecordToOriginalFormat nucio deltaRecordHeaderToString deltaAlignmentHeaderToString N/A N/A N/A N/A len N/A sys argv 6 N/A N/A N/A N/A sys exit pre_delta_filter.py in.delta wiggle_pct contained_pct min_alignment_size out_file alignment_is_good N/A N/A record a arange N/A N/A N/A trimmed_slen N/A N/A arange end N/A arange start N/A N/A trimmed_slen 0 N/A N/A N/A N/A sys exit BUG: trimmed_slen bad value
 N/A qury_wiggle N/A N/A record qlen WIGGLE_PCT N/A N/A N/A N/A fabs N/A N/A a send N/A a sstart MIN_ALIGNMENT_SIZE N/A N/A False N/A N/A N/A N/A fabs N/A N/A a send N/A a sstart N/A trimmed_slen CONTAINED_PCT N/A N/A record qlen N/A record slen N/A N/A True N/A N/A N/A N/A fabs N/A N/A a qend N/A a qstart N/A N/A record qlen CONTAINED_PCT N/A N/A record slen N/A record qlen N/A N/A True N/A N/A N/A N/A N/A a sstart N/A arange start N/A N/A arange end N/A a send N/A N/A N/A a qstart qury_wiggle N/A N/A a qend qury_wiggle N/A N/A N/A record qlen N/A a qstart qury_wiggle N/A N/A N/A record qlen N/A a qend qury_wiggle N/A N/A True N/A False N/A N/A AlignmentRange N/A namedtuple AlignmentRange N/A start end N/A WIGGLE_PCT N/A float N/A N/A sys argv N/A 2 N/A CONTAINED_PCT N/A float N/A N/A sys argv N/A 3 N/A MIN_ALIGNMENT_SIZE N/A int N/A N/A sys argv N/A 4 N/A outfilename N/A N/A sys argv N/A 5 N/A fh N/A open N/A N/A sys argv N/A 1 N/A delta_header N/A N/A N/A fh readline N/A N/A N/A N/A fh readline strip N/A deltaHash N/A N/A record N/A getDeltaAlignmentIterator fh N/A N/A N/A N/A N/A deltaHash has_key N/A record sname N/A N/A N/A deltaHash N/A N/A record sname N/A N/A N/A N/A N/A deltaHash N/A N/A record sname append record N/A N/A N/A fh close N/A readRange N/A N/A N/A readname drecord_list N/A N/A deltaHash iteritems N/A N/A N/A start end N/A N/A N/A drecord_list N/A 0 slen 0 N/A drecord drecord_list N/A N/A alignment N/A drecord alignments N/A N/A l N/A min N/A alignment sstart N/A alignment send N/A N/A l start N/A N/A start l N/A r N/A max N/A alignment sstart N/A alignment send N/A N/A r end N/A N/A end r N/A N/A readRange N/A readname N/A AlignmentRange start end N/A ofh N/A open outfilename w N/A efh N/A open N/A outfilename .log w N/A N/A N/A ofh write delta_header N/A N/A N/A ofh write N/A N/A readname drecord_list N/A N/A deltaHash iteritems N/A N/A alignment_range N/A readRange N/A readname N/A record drecord_list N/A N/A pfalignments N/A N/A alnmt N/A record alignments N/A N/A N/A alignment_is_good record alnmt alignment_range N/A N/A N/A N/A pfalignments append alnmt N/A N/A N/A N/A efh write Remove Alignment:
 N/A N/A N/A efh write N/A N/A deltaRecordHeaderToString record N/A N/A N/A efh write N/A N/A deltaAlignmentHeaderToString alnmt N/A N/A N/A len pfalignments 1 N/A N/A N/A N/A efh write Multiple Alignments
 N/A N/A N/A efh write N/A N/A deltaRecordHeaderToString record N/A a pfalignments N/A N/A N/A N/A efh write N/A N/A deltaAlignmentHeaderToString a N/A N/A N/A record alignments N/A N/A N/A al pfalignments N/A N/A N/A N/A N/A record alignments append al N/A N/A N/A len N/A record alignments 0 N/A N/A N/A N/A ofh write N/A deltaRecordToOriginalFormat record N/A N/A N/A ofh write N/A N/A N/A efh close N/A N/A N/A ofh close