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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 1.06 (Full Release on 4/17/2013) ==
'''Variant Calling'''
* Update to always require REF
** this fixes bug that ''ldrefine'' was not checking REF or adding the optional prefix to it.
== Version 1.05 (Full Release on 4/17/2013) ==
== Version 1.05 (Full Release on 4/17/2013) ==
''Aligner & SnpCalling'''
''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
** Now used for index files & reference files in addition to fastqs (aligner) and bams (snpcalling)
** Now used for index files & reference files in addition to fastqs (aligner) and bams (variant calling)
== Version 1.04 (Full Release on 4/16/2013) ==
== Version 1.04 (Full Release on 4/16/2013) ==
'''Aligner & UMAKE/snpcalling'''
'''Aligner & Variant Calling'''
* Update relative paths to be relative to the current working directory
* Update relative paths to be relative to the current working directory
** Aligner effects:
** Aligner effects:
*** INDEX_FILE as specified in the aligner configuration
*** INDEX_FILE as specified in the aligner configuration
*** fastq paths specified in the INDEX_FILE
*** fastq paths specified in the INDEX_FILE
** UMAKE/snpcalling effects:
** Variant Calling effects:
** BAM_INDEX as specified in the configuration
** BAM_INDEX as specified in the configuration
** bam paths specified in the BAM_INDEX
** bam paths specified in the BAM_INDEX
** FASTQ_PREFIX (for aligner reading the fastq index file)
** FASTQ_PREFIX (for aligner reading the fastq index file)
*** renamed from FASTQ/FASTQ_REF
*** renamed from FASTQ/FASTQ_REF
** BAM_PREFIX (for umake/snpcalling reading bam index file)
** BAM_PREFIX (for variant calling reading bam index file)
* Improve Error detection
* Improve Error detection
** With --test option, check that the testdir exists before running the test
** With --test option, check that the testdir exists before running the test
** Also add support for fixing the problem with UMich directories when using Mosix
** Also add support for fixing the problem with UMich directories when using Mosix
* Update the default Reference directory to be as expected for UM
* Update the default Reference directory to be as expected for UM
* snpcalling changes:
* Variant Calling changes:
** SVM
** SVM
*** Add option to merge all chromosome sites prior to running SVM (to better support targeted sequencing)
*** Add option to merge all chromosome sites prior to running SVM (to better support targeted sequencing)
* Add pre-checks for required files & reference files prior to running
* Add pre-checks for required files & reference files prior to running
* Add checks for deprecated configuration settings
* Add checks for deprecated configuration settings
* Merge aligner & snpcalling default configurations into a single file (bin/gotcloudDefaults.conf)
* Merge aligner & variant calling default configurations into a single file (bin/gotcloudDefaults.conf)
* Aligner
* Aligner
** Update to put actual values into the Makefile recipes rather than using variables
** Update to put actual values into the Makefile recipes rather than using variables
* SnpCalling
* Variant Calling
** Fix vcf-summary to handle chromosomes that have string names (like X,Y)
** Fix vcf-summary to handle chromosomes that have string names (like X,Y)
== Version 1.03a4 (Internal Only Release on 4/2/2013) ==
== Version 1.03a4 (Internal Only Release on 4/2/2013) ==
* snpCalling:
* Variant Calling:
** Update to by default run as local
** Update to by default run as local
** Target Loci file updates:
** Target Loci file updates:
== Version 1.03a1 (Internal Only Release on 3/26/2013) ==
== Version 1.03a1 (Internal Only Release on 3/26/2013) ==
* SnpCall
* Variant Calling
** Add FILTER_MIN_NS to add the option of filtering based on the number of samples
** Add FILTER_MIN_NS to add the option of filtering based on the number of samples
** Add FILTER_ADDITIONAL to add the option of adding additional filters.
** Add FILTER_ADDITIONAL to add the option of adding additional filters.
== Version 1.03a (Full Release on 3/22/2913) ==
== Version 1.03a (Full Release on 3/22/2913) ==
* Cleanup README & INSTALL instructions
* Cleanup README & INSTALL instructions
* SnpCall
* Variant Calling
** Fix dependency bug/error in SVM
** Fix dependency bug/error in SVM
** Fix commands that run locally to check for pipe failures
** Fix commands that run locally to check for pipe failures
