Module Expr Str Import alias Import alias Import alias ImportFrom alias ImportFrom alias Import alias ClassDef bases AttributeLoad NameLoad attr body FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad ListLoad Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str keyword ListLoad TupleLoad Str Num TupleLoad Str Num Assign NameStore Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str keyword NameLoad Assign NameStore Call AttributeLoad Str attr Str Str Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad ListLoad Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Assign NameStore Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str keyword NameLoad Assign NameStore Call AttributeLoad Str attr Str Str Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad ListLoad Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str keyword ListLoad TupleLoad Str Num TupleLoad Str Num Assign NameStore Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str keyword Num keyword NameLoad Assign NameStore Call AttributeLoad Str attr Str Str Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad ListLoad Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str keyword NameLoad Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Assign NameStore Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str keyword NameLoad keyword NameLoad Assign NameStore Call AttributeLoad Str attr Str Str Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad ListLoad Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str keyword NameLoad Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Assign NameStore Call NameLoad keyword Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Str Str Assign NameStore Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str keyword NameLoad keyword NameLoad keyword NameLoad Assign NameStore Call AttributeLoad Str attr Str Str Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad ListLoad Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str keyword NameLoad Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Assign NameStore Call NameLoad keyword Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Str Str Assign NameStore Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str keyword NameLoad keyword NameLoad keyword NameLoad Assign NameStore Call AttributeLoad Str attr Str Str Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad ListLoad Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Assign NameStore Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str keyword NameLoad keyword NameLoad Assign NameStore Call AttributeLoad Str attr Str Str Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad ListLoad Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Assign NameStore Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str keyword NameLoad keyword NameLoad keyword NameLoad Assign NameStore Call AttributeLoad Str attr Str Str Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad ListLoad Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str Expr Call AttributeLoad NameLoad attr Str Str Str Num Num keyword Str keyword ListLoad TupleLoad Str Num TupleLoad Str Num Assign NameStore Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str keyword Num keyword NameLoad Assign NameStore Call AttributeLoad Str attr Str Str Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad NameLoad attr Num Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Num Num Num Num Expr Call AttributeLoad NameLoad attr Num Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Num Num Num Num Expr Call AttributeLoad NameLoad attr Num Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Num Num Num Num decorator_list decorator_list If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr
N/A N/A 
Tests for bamutils basecall
 N/A os N/A StringIO N/A unittest ngsutils.bam.t MockBam ngsutils.bed BedFile N/A ngsutils.bam.basecall BaseCallTest N/A N/A unittest TestCase N/A testBaseCall N/A N/A self N/A N/A N/A bam N/A MockBam N/A test2 N/A N/A N/A bam add_read foo1 atcgatcg ........ 0 0 cigar 8M N/A N/A N/A bam add_read foo2 atcgatcg AAAAAAAA 0 4 cigar 8M N/A N/A N/A bam add_read foo3 accgatcg ######## 0 4 cigar 8M tags N/A N/A IH 2 N/A HI 1 N/A out N/A N/A StringIO StringIO N/A N/A N/A N/A N/A ngsutils bam basecall bam_basecall bam N/A N/A N/A os path join N/A N/A N/A os path dirname __file__ test.fa out out N/A valid N/A N/A chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts
test2|1|A|1|A||1.0|0.91686730441|1|0|0|0|0|0|0|0|
test2|2|T|1|T||1.0|3.25488750216|0|0|0|1|0|0|0|0|
test2|3|C|1|C||1.0|3.25488750216|0|1|0|0|0|0|0|0|
test2|4|G|1|G||1.0|0.91686730441|0|0|1|0|0|0|0|0|
test2|5|A|3|A||1.33333333333|1.65545182665|3|0|0|0|0|0|0|0|
test2|6|T|3|T|C|1.33333333333|2.9097148334|0|1|0|2|0|0|0|0|
test2|7|C|3|C||1.33333333333|4.85048518563|0|3|0|0|0|0|0|0|
test2|8|G|3|G||1.33333333333|1.65545182665|0|0|3|0|0|0|0|0|
test2|9|A|2|A||1.5|1.36179536943|2|0|0|0|0|0|0|0|
test2|10|T|2|T||1.5|4.24102241591|0|0|0|2|0|0|0|0|
test2|11|C|2|C||1.5|4.24102241591|0|2|0|0|0|0|0|0|
test2|12|G|2|G||1.5|1.36179536943|0|0|2|0|0|0|0|0|
 replace | N/A N/A N/A self assertEqual valid N/A N/A out getvalue N/A testBaseCallInDel N/A N/A self N/A N/A N/A bam N/A MockBam N/A test2 N/A N/A N/A bam add_read foo1 atcgaTtcg ......... 0 0 cigar 5M1I3M N/A N/A N/A bam add_read foo2 atcgacg AAAAAAA 0 4 cigar 5M1D2M N/A out N/A N/A StringIO StringIO N/A N/A N/A N/A N/A ngsutils bam basecall bam_basecall bam N/A N/A N/A os path join N/A N/A N/A os path dirname __file__ test.fa out out N/A valid N/A N/A chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts
test2|1|A|1|A||1.0|0.91686730441|1|0|0|0|0|0|0|0|
test2|2|T|1|T||1.0|3.25488750216|0|0|0|1|0|0|0|0|
test2|3|C|1|C||1.0|3.25488750216|0|1|0|0|0|0|0|0|
test2|4|G|1|G||1.0|0.91686730441|0|0|1|0|0|0|0|0|
test2|5|A|2|A||1.0|1.36179536943|2|0|0|0|0|0|0|0|
test2|6|T|2|T||1.0|4.24102241591|0|0|0|2|0|0|0|1|T:1
test2|7|C|2|C||1.0|4.24102241591|0|2|0|0|0|0|0|0|
test2|8|G|2|G||1.0|1.36179536943|0|0|2|0|0|0|0|0|
test2|9|A|1|A||1.0|0.91686730441|1|0|0|0|0|0|0|0|
test2|10|T|0|N||1.0|0|0|0|0|0|0|1|0|0|
test2|11|C|1|C||1.0|3.25488750216|0|1|0|0|0|0|0|0|
test2|12|G|1|G||1.0|0.91686730441|0|0|1|0|0|0|0|0|
 replace | N/A N/A N/A self assertEqual valid N/A N/A out getvalue N/A testBaseCallMinQual N/A N/A self N/A N/A N/A bam N/A MockBam N/A test2 N/A N/A N/A bam add_read foo1 atcgatcg ........ 0 0 cigar 8M N/A N/A N/A bam add_read foo2 atcgatcg AAAAAAAA 0 4 cigar 8M N/A N/A N/A bam add_read foo3 accgatcg ######## 0 4 cigar 8M tags N/A N/A IH 2 N/A HI 1 N/A out N/A N/A StringIO StringIO N/A N/A N/A N/A N/A ngsutils bam basecall bam_basecall bam N/A N/A N/A os path join N/A N/A N/A os path dirname __file__ test.fa min_qual 10 out out N/A valid N/A N/A chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts
test2|1|A|1|A||1.0|0.91686730441|1|0|0|0|0|0|0|0|
test2|2|T|1|T||1.0|3.25488750216|0|0|0|1|0|0|0|0|
test2|3|C|1|C||1.0|3.25488750216|0|1|0|0|0|0|0|0|
test2|4|G|1|G||1.0|0.91686730441|0|0|1|0|0|0|0|0|
test2|5|A|2|A||1.0|1.36179536943|2|0|0|0|0|0|0|0|
test2|6|T|2|T||1.0|4.24102241591|0|0|0|2|0|0|0|0|
test2|7|C|2|C||1.0|4.24102241591|0|2|0|0|0|0|0|0|
test2|8|G|2|G||1.0|1.36179536943|0|0|2|0|0|0|0|0|
test2|9|A|1|A||1.0|0.91686730441|1|0|0|0|0|0|0|0|
test2|10|T|1|T||1.0|3.25488750216|0|0|0|1|0|0|0|0|
test2|11|C|1|C||1.0|3.25488750216|0|1|0|0|0|0|0|0|
test2|12|G|1|G||1.0|0.91686730441|0|0|1|0|0|0|0|0|
 replace | N/A N/A N/A self assertEqual valid N/A N/A out getvalue N/A testBaseCallStrand N/A N/A self N/A N/A N/A bam N/A MockBam N/A test2 N/A N/A N/A bam add_read foo1 atcgatcg ........ 0 0 cigar 8M N/A N/A N/A bam add_read foo2 atcgatcg AAAAAAAA 0 4 cigar 8M N/A N/A N/A bam add_read foo3 accgatcg ######## 0 4 cigar 8M is_reverse True N/A N/A N/A bam add_read foo4 atcgactgatcg ############ 0 0 cigar 12M N/A out N/A N/A StringIO StringIO N/A N/A N/A N/A N/A ngsutils bam basecall bam_basecall bam N/A N/A N/A os path join N/A N/A N/A os path dirname __file__ test.fa showstrand True out out N/A valid N/A N/A chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts|+ strand %|A minor %|C minor %|G minor %|T minor %|N minor %|Deletion minor %|Insertion minor %
test2|1|A|2|A||1.0|1.36179536943|2|0|0|0|0|0|0|0||1.0|0.0|0.0|0.0|0.0|0.0|0.0|0.0
test2|2|T|2|T||1.0|4.24102241591|0|0|0|2|0|0|0|0||1.0|0.0|0.0|0.0|0.0|0.0|0.0|0.0
test2|3|C|2|C||1.0|4.24102241591|0|2|0|0|0|0|0|0||1.0|0.0|0.0|0.0|0.0|0.0|0.0|0.0
test2|4|G|2|G||1.0|1.36179536943|0|0|2|0|0|0|0|0||1.0|0.0|0.0|0.0|0.0|0.0|0.0|0.0
test2|5|A|4|A||1.0|1.87433193885|4|0|0|0|0|0|0|0||0.75|0.25|0.0|0.0|0.0|0.0|0.0|0.0
test2|6|T|4|T/C||1.0|2.94335833285|0|2|0|2|0|0|0|0||0.75|0.0|0.5|0.0|0.0|0.0|0.0|0.0
test2|7|C|4|C|T|1.0|3.45990045591|0|3|0|1|0|0|0|0||0.75|0.0|0.333333333333|0.0|0.0|0.0|0.0|0.0
test2|8|G|4|G||1.0|1.87433193885|0|0|4|0|0|0|0|0||0.75|0.0|0.0|0.25|0.0|0.0|0.0|0.0
test2|9|A|3|A||1.0|1.65545182665|3|0|0|0|0|0|0|0||0.666666666667|0.333333333333|0.0|0.0|0.0|0.0|0.0|0.0
test2|10|T|3|T||1.0|4.85048518563|0|0|0|3|0|0|0|0||0.666666666667|0.0|0.0|0.0|0.333333333333|0.0|0.0|0.0
test2|11|C|3|C||1.0|4.85048518563|0|3|0|0|0|0|0|0||0.666666666667|0.0|0.333333333333|0.0|0.0|0.0|0.0|0.0
test2|12|G|3|G||1.0|1.65545182665|0|0|3|0|0|0|0|0||0.666666666667|0.0|0.0|0.333333333333|0.0|0.0|0.0|0.0
 replace | N/A N/A N/A self assertEqual valid N/A N/A out getvalue N/A testBaseCallRegion N/A N/A self N/A N/A N/A bam N/A MockBam N/A test2 N/A N/A N/A bam add_read foo1 atcgatcg ........ 0 0 cigar 8M N/A N/A N/A bam add_read foo2 atcgatcg AAAAAAAA 0 4 cigar 8M N/A N/A N/A bam add_read foo3 accgatcg ######## 0 4 cigar 8M is_reverse True N/A N/A N/A bam add_read foo4 atcgactgatcg ############ 0 0 cigar 12M N/A bed N/A BedFile fileobj N/A N/A StringIO StringIO N/A N/A test2|4|7
 replace | N/A out N/A N/A StringIO StringIO N/A N/A N/A N/A N/A ngsutils bam basecall bam_basecall bam N/A N/A N/A os path join N/A N/A N/A os path dirname __file__ test.fa showstrand True regions bed out out N/A valid N/A N/A chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts|+ strand %|A minor %|C minor %|G minor %|T minor %|N minor %|Deletion minor %|Insertion minor %
test2|5|A|4|A||1.0|1.87433193885|4|0|0|0|0|0|0|0||0.75|0.25|0.0|0.0|0.0|0.0|0.0|0.0
test2|6|T|4|T/C||1.0|2.94335833285|0|2|0|2|0|0|0|0||0.75|0.0|0.5|0.0|0.0|0.0|0.0|0.0
test2|7|C|4|C|T|1.0|3.45990045591|0|3|0|1|0|0|0|0||0.75|0.0|0.333333333333|0.0|0.0|0.0|0.0|0.0
test2|8|G|4|G||1.0|1.87433193885|0|0|4|0|0|0|0|0||0.75|0.0|0.0|0.25|0.0|0.0|0.0|0.0
 replace | N/A N/A N/A self assertEqual valid N/A N/A out getvalue N/A testBaseCallRegionStrand N/A N/A self N/A N/A N/A bam N/A MockBam N/A test2 N/A N/A N/A bam add_read foo1 atcgatcg ........ 0 0 cigar 8M N/A N/A N/A bam add_read foo2 atcgatcg AAAAAAAA 0 4 cigar 8M N/A N/A N/A bam add_read foo3 accgatcg ######## 0 4 cigar 8M is_reverse True N/A N/A N/A bam add_read foo4 atcgactgatcg ############ 0 0 cigar 12M N/A bed N/A BedFile fileobj N/A N/A StringIO StringIO N/A N/A test2|4|7|foo|1|-
 replace | N/A out N/A N/A StringIO StringIO N/A N/A N/A N/A N/A ngsutils bam basecall bam_basecall bam N/A N/A N/A os path join N/A N/A N/A os path dirname __file__ test.fa showstrand True regions bed out out N/A valid N/A N/A chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts|+ strand %|A minor %|C minor %|G minor %|T minor %|N minor %|Deletion minor %|Insertion minor %
test2|5|A|4|A||1.0|1.87433193885|4|0|0|0|0|0|0|0||0.75|0.25|0.0|0.0|0.0|0.0|0.0|0.0
test2|6|T|4|T/C||1.0|2.94335833285|0|2|0|2|0|0|0|0||0.75|0.0|0.5|0.0|0.0|0.0|0.0|0.0
test2|7|C|4|C|T|1.0|3.45990045591|0|3|0|1|0|0|0|0||0.75|0.0|0.333333333333|0.0|0.0|0.0|0.0|0.0
test2|8|G|4|G||1.0|1.87433193885|0|0|4|0|0|0|0|0||0.75|0.0|0.0|0.25|0.0|0.0|0.0|0.0
 replace | N/A N/A N/A self assertEqual valid N/A N/A out getvalue N/A testBaseCallVariants N/A N/A self N/A N/A N/A bam N/A MockBam N/A test2 N/A N/A N/A bam add_read foo1 atcgaccg ........ 0 0 cigar 8M N/A N/A N/A bam add_read foo2 atcgattg AAAAAAAA 0 4 cigar 8M N/A N/A N/A bam add_read foo3 accgattg ######## 0 4 cigar 8M N/A out N/A N/A StringIO StringIO N/A N/A N/A N/A N/A ngsutils bam basecall bam_basecall bam N/A N/A N/A os path join N/A N/A N/A os path dirname __file__ test.fa variants True out out N/A valid N/A N/A chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts
test2|6|T|3|C|T|1.0|2.9097148334|0|2|0|1|0|0|0|0|
test2|11|C|2|T||1.0|4.24102241591|0|0|0|2|0|0|0|0|
 replace | N/A N/A N/A self assertEqual valid N/A N/A out getvalue N/A testBaseCallHetTest N/A N/A self N/A N/A N/A bam N/A MockBam N/A test2 N/A N/A N/A bam add_read foo1 atcgaccg ........ 0 0 cigar 8M N/A N/A N/A bam add_read foo2 atcgattg AAAAAAAA 0 4 cigar 8M N/A N/A N/A bam add_read foo3 accgattg ######## 0 4 cigar 8M N/A out N/A N/A StringIO StringIO N/A N/A N/A N/A N/A ngsutils bam basecall bam_basecall bam N/A N/A N/A os path join N/A N/A N/A os path dirname __file__ test.fa variants True hettest True out out N/A valid N/A N/A chrom|pos|ref|count|consensus call|minor call|ave mappings|alt. allele freq|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts
test2|6|T|3|C|T|1.0|0.333333333333|2.9097148334|0|2|0|1|0|0|0|0|
test2|11|C|2|T||1.0|0.0|4.24102241591|0|0|0|2|0|0|0|0|
 replace | N/A N/A N/A self assertEqual valid N/A N/A out getvalue N/A testBaseCallMinCount N/A N/A self N/A N/A N/A bam N/A MockBam N/A test2 N/A N/A N/A bam add_read foo1 atcgatcg ........ 0 0 cigar 8M N/A N/A N/A bam add_read foo2 atcgatcg AAAAAAAA 0 4 cigar 8M N/A N/A N/A bam add_read foo3 accgatcg ######## 0 4 cigar 8M tags N/A N/A IH 2 N/A HI 1 N/A out N/A N/A StringIO StringIO N/A N/A N/A N/A N/A ngsutils bam basecall bam_basecall bam N/A N/A N/A os path join N/A N/A N/A os path dirname __file__ test.fa min_count 2 out out N/A valid N/A N/A chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts
test2|5|A|3|A||1.33333333333|1.65545182665|3|0|0|0|0|0|0|0|
test2|6|T|3|T|C|1.33333333333|2.9097148334|0|1|0|2|0|0|0|0|
test2|7|C|3|C||1.33333333333|4.85048518563|0|3|0|0|0|0|0|0|
test2|8|G|3|G||1.33333333333|1.65545182665|0|0|3|0|0|0|0|0|
test2|9|A|2|A||1.5|1.36179536943|2|0|0|0|0|0|0|0|
test2|10|T|2|T||1.5|4.24102241591|0|0|0|2|0|0|0|0|
test2|11|C|2|C||1.5|4.24102241591|0|2|0|0|0|0|0|0|
test2|12|G|2|G||1.5|1.36179536943|0|0|2|0|0|0|0|0|
 replace | N/A N/A N/A self assertEqual valid N/A N/A out getvalue N/A testHeterzygosity N/A N/A self N/A N/A N/A N/A N/A self assertEqual 0.0 N/A N/A N/A N/A ngsutils bam basecall _calculate_heterozygosity 10 5 5 0 N/A N/A N/A self assertEqual 0.5 N/A N/A N/A N/A ngsutils bam basecall _calculate_heterozygosity 5 5 0 0 N/A N/A N/A self assertEqual 0.1 N/A N/A N/A N/A ngsutils bam basecall _calculate_heterozygosity 9 1 0 0 N/A N/A N/A N/A __name__ __main__ N/A N/A N/A N/A unittest main