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samtools/htsjdk

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getAnyAttribute returns String instead of List<Integer>
#958 opened Jul 29, 2017 by dariober

2
Missing value in integer FORMAT field returns -1
#957 opened Jul 28, 2017 by dariober

2
Remove SAMTools.jar after one/two releases
#955 opened Jul 28, 2017 by magicDGS
Proposal: deprecate SQTagUtil.java
#949 opened Jul 27, 2017 by magicDGS
Can't read or write gzipped BCFs
#946 opened Jul 26, 2017 by cmnbroad
LocationAware implementations should honor getPosition contract
#945 opened Jul 25, 2017 by cmnbroad
TribbleIndexReader stream management should be audited
#944 opened Jul 25, 2017 by cmnbroad
BinningIndexBuilder assumes no feature can be at offset 0
#943 opened Jul 24, 2017 by cmnbroad

3
Add ability to log to file
#941 opened Jul 24, 2017 by ronlevine

1
Performance issues with VCF header parsing
#934 opened Jul 14, 2017 by SquidDev

1
Extend allele frequencies calculation to use sample genotypes
#930 opened Jul 7, 2017 by cyenyxe

1
equals in VCFInfoHeaderLine is using description.equals(other.description) ?
#929 opened Jul 7, 2017 by lindenb

6
Port picard's LiftoverVcf.leftAlignVariant
#925 opened Jul 3, 2017 by magicDGS

3
Add option to use the maximum instead of the first overlap for LiftOver
#924 opened Jun 30, 2017 by ronlevine
Pruning list of people with admin & write access to the project
#923 opened Jun 29, 2017 by tfenne

11
Genotype.hasAnyAttribute() should not always return true for FT
#920 opened Jun 28, 2017 by ronlevine
Deprecate SortingVariantContextWriter and SortingVariantContextWriterBase
#919 opened Jun 27, 2017 by yfarjoun
Error executing two sequential SamReader.queryOverlapping() calls for a CRAM File
#918 opened Jun 26, 2017 by skashin
Mixed licensing is unfortunate; can we remedy this?
#917 opened Jun 26, 2017 by tfenne

5
TabixReader bug in query(String) method for coordiantes with 0 values
#908 opened Jun 22, 2017 by phanikishore2

4
Support for partial VCF writing - htsget extension for VCF
#902 opened Jun 19, 2017 by cyenyxe
Support for long reference sequences
#900 opened Jun 15, 2017 by jayoung

7
SeekableStream subclasses should implement InputStream.available()
#898 opened Jun 9, 2017 by lbergelson
Proposal: separate HTSJDK in different gradle build artifacts
#896 opened Jun 9, 2017 by magicDGS

1
Remove SRA code from htsjdk
#894 opened Jun 9, 2017 by yfarjoun

11

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