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For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems|FAQ: Version Problems]]
For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems|FAQ: Version Problems]]
== Version 1.14 (Full Release on 8/29/2014) ==
'''General'''
* Add initial beagle4 support (as a new pipeline)
* Improve input validation
** Add chromosome name consistency checks to all tools
* Upgrade version of bgzf
* Upgrade libStatGen to fix mergeBam issue.
'''Aligner'''
* Cleanup reading of fastq index/info file
** ignore empty lines (generates a warning)
** compress extra tabs/trim white space
* Validate that BWA_QUAL and BWA_THREADS settings are properly formatted
'''SnpCall'''
* Replace glfMultiples with glfFlex
* Validate format of BAM_INDEX file
* Add INDEL_VCF as an alternate for INDEL_PREFIX for input indel vcfs that aren't split by chromosome.
'''Genotype Refinement'''
* Only run beagle/thunder with more than 1 sample
'''Indel'''
* mergeBams for a single sample as its own step (didn't work before)
* Fix bug that it would fail if the list of files was too long
* Add input validation
* Validate format of BAM_INDEX file
== Version 1.13 (Full Release on 7/15/2014) ==
== Version 1.13 (Full Release on 7/15/2014) ==
