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This queue is for tickets about the Bio-SamTools CPAN distribution.

Maintainer(s)

LDS

Bugs

ID Subject Status Severity Last Updated Broken in Fixed in
57143 Deletions in Pileup new 10 years ago
54392 CQ tag bug new 10 years ago
101735 Bio::DB:Sam won't read a particular BAM file open 5 years ago
52363 Inconsistent return values in Bio::DB::Sam->features method new 11 years ago 1.07
81949 Documentation bug open 5 years ago
49986 seq_ids returns only lower-case entry names open 11 years ago
110409 Module v1.4.2 bug new 5 years ago
88947 Re: Suggested patch for installation failure to find samtools headers in include/bam/ path new 7 years ago
84656 Trouble installing BIo:DB:SAM tools new 7 years ago
66209 Suggested change to coverage_from_pileup_fun in Sam.xs new 9 years ago
106384 Bio-SamTools run error open 5 years ago
53705 $index undefined prior to coverage call new 11 years ago
101733 bam2bedgraph compile error (Fedora 21, stock gcc, etc.) open 5 years ago
51485 Missing character->value conversion in example SNP caller? new 11 years ago
116702 Re: Bio-SamTools-1.43 is confused about what various SAMtools build dirs supply where - and so am I new 4 years ago
101438 CIGAR parsing error in Bio::DB::Sam new 6 years ago
87175 Bio::DB::Sam problems new 7 years ago
68400 Uninstalling old version of Bio::DB::Sam new 9 years ago
66138 _coverage function should not count reads that skip the input region new 9 years ago
54411 Re: CQ tag bug new 10 years ago
105418 Compile error under CentOS 6.6 open 5 years ago
52905 Bio::DB::Sam objects crashes threads new 11 years ago
98692 Feature request: support for samtools v1.0 open 5 years ago
50532 Sam.pm croaks wrong path if not -e $bam_path open 11 years ago
116683 Bio-SamTools-1.43 is confused about what various SAMtools build dirs supply where - and so am I new 4 years ago
89192 feature request: accessor for low level Alignment in AlignmentWrapper new 7 years ago
86069 Suggested patch for installation failure to find samtools headers in include/bam/ path new 7 years ago
66387 Need to process CIGAR N in dna function new 9 years ago
69903 Coverage and pileup functions corrupted by samtools core open Critical 9 years ago 1.29
54562 Bio::DB::Sam segfaults when reading a BAM file without reading the header first new Important 10 years ago 1.10
83974 max_pileup_cnt should be raised for coverage2bedGraph new Important 7 years ago 1.31
1.32
1.33
1.35
1.36
1.37
76279 -filter option doesn't function as documented (deprecated AUTOLOAD) new Important 8 years ago 1.33
81118 Test failed for Bio::DB::Sam new Important 8 years ago 1.36
50653 Error in gbrowse2: Method abs_ref missing new Unimportant 11 years ago 1.05
80688 behaviour of qpos in deletion regions new Wishlist 8 years ago 1.36
73737 Allow calmd be called on an Alignment? new Wishlist 9 years ago
73781 Debian binary-without-manpage lintian warning new Wishlist 9 years ago 1.33

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