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For information on installing the releases, see: [[GotCloud#Install_GotCloud_Software|Install GotCloud Software]]
For information on installing the releases, see: [[GotCloud#Install_GotCloud_Software|Install GotCloud Software]]
== Version 1.07 (Full Release on 7/3/2013) ==
'''Aligner'''
* DEPRECATED:
** BWA_MAX_MEM is now SORT_MAX_MEM
** VERIFY_BAM_ID_OPTIONS is now
**
* Upgrade to latest QPLOT
** GC Content file has been renamed to have the extension: .winsize100.gc
* Automatically generates the bam index file if BAM_INDEX is specified
* Run DEDUP & RECAB as 1 step instead of 2
* Update dedup, recab, qplot, & verifyBamID steps to be specified via configuration
** Easier to insert steps between/before/after these
* Fixed bug where the merge failed if there was only 1 fastq pair
* Improve informational messages
* Update to BWA version 0.6.1-r104
* Bring in mergeBam updates from latest bamUtil
** ignore PG lines with duplicate ids
* General code cleanup
* Add some Mosaik support
** Added support to align.pl and a way to enable it, but the code doesn't compile
* Calculate approximate storage needed for GotCloud so user can have an idea what is coming
* Makefile now uses bash and pipefail to catch errors that occur within piped commands
* Removed the md5sum calculation
'''Variant Calling'''
* Update to always require REF
** this fixes bug that ''ldrefine'' was not checking REF or adding the optional prefix to it.
* SVM - fib bug on qual check in run_libsvm.pl
* Update defaults for filtering
* Fixed bug in libVcf/VcfFile that had FamID instead of FatID
* Fixed bug in samtools-hybrid that caused it to fail when checking for BAI files if bam was elsewhere in the filename
* Fix vcfPielup to accept .bam.bai or .bai in bam index filenames.
* Fix the split logic to work if a VCF file had no PASS records
'''Aligner & Variant Calling'''
* Add checks for required executables prior to running
* Limit the number of jobs that can run locally (there is a flag to override this)
* Extract configuration routines from the 2 .pl's to a common Conf.pm
* Add FLUX support
== Version 1.06 (Full Release on 4/17/2013) ==
== Version 1.06 (Full Release on 4/17/2013) ==
== Version 1.05 (Full Release on 4/17/2013) ==
== Version 1.05 (Full Release on 4/17/2013) ==
''Aligner & Variant Calling'''
'''Aligner & Variant Calling'''
* Cleanup handling of BASE_PREFIX & added REF_PREFIX.
* Cleanup handling of BASE_PREFIX & added REF_PREFIX.
** Allows user to specify --base_prefix or --baseprefix on command-line
** Allows user to specify --base_prefix or --baseprefix on command-line
