ASAP Changelist V1.1.2

The following items have been changed/corrected or added in version 1.1.2 of ASAP.
Item Notes Date Completed
Alignment caused failures under certain circumentances Fixed an error where some conditions would cause ASAP to instruct samtools to index .bai files, which caused an error. Jun 27, 2012
Corrected status reporting Fixed a database query error preventing ASAP from correctly getting job lists based on status in certain situations. This affected several job related tools, such as STATUS, RECONCILE and SHOW_LOG Jun 27, 2012

ASAP Changelist V1.1.1

The following items have been changed/corrected or added in version 1.0.1 of ASAP.
Item Notes Date Completed
Basic summary for BAMs Added flagstat summary for bam files Jun 25, 2012
Bug fixes for PREP_SYSTEM Some issues with certain cases involving GATK and Picard getting linked improperly Jun 20, 2012
Issue with chgrp fixed ACCRE changed some security which caused chgrp to fail when performed within a cluster based job. Switched to using group sticky bit for all executors. Jun 20, 2012

ASAP Changelist V1.1.0

The following items have been changed/corrected or added in version 1.0.1 of ASAP.
Item Notes Date Completed
PREP_SYSTEM added Provide a method to allow the user to install tools using ASAP to simplify getting started Jun 12, 2012
Added halt feature when tools were outdated Previously, versions were simply reported. Now, ASAP will halt if the versions are older than expected. Jun 12, 2012

ASAP Changelist V1.1.0

The following items have been changed/corrected or added in version 1.0.1 of ASAP.
Item Notes Date Completed
infer Final/Intermed Dirs When generating sample configurations, ASAP now infers the location based on the CWD. This can be overridden by the user once they edit the configuration, but follows the standard approach we've been using internally. May 10, 2012
additional flags added Added flags for setting PICARD_PATH to allow users to set these paths during sample generation May 10, 2012
GENERATE_BATCH is slightly more tolerant of naming Added support for lower case "r" in paired end designation, and also expressly fails if the translation from 1 to 2 results in no change to the filename May 10, 2012
Removed Vanderbilt specific paths from a default setting The reference sequence had the default path to our local reference. That has been removed and defaults to an empty string May 10, 2012
Added some cmd line options Added command line options to simplify the generation of new configuration files. These include: PICARD_PATH. May 11, 2012
Accept relative paths for Reference Allow the user to specify reference sequence using relative path May 11, 2012
Relative defaults for FINAL and INTERMEDIATE If these don't exist as part of configuration or cmd-line, the program uses the current working directory to "bake" valid settings within the current directory. May 11, 2012
Added IMPORT_BAM functionality Users can import bam files as either aligned, realigned or recalibrated and they will fit into the pipeline as if they were processed by the application itself May 18, 2012
Added INDEL Users can call Indels using GATK (samtools to come very soon) May 22, 2012
Added support for annotations via Annovar Users can now utilize most annovar functionality after VCFs have been produced (indel and SNP) May 22, 2012
Improved Serial Execution Added halt on error to serial execution along with automatic start after scripts are generated (-j like cluster based autosubmit) May 22, 2012
Minor changes to database to allow concurrent steps to be run simultaneously This was necessary for INDEL/SNP parallel execution. As a result, most step's ranks were updated to be consistent for each primary step May 22, 2012
Executor Verification Check for group settings in configuration May 23, 2012
Options for MarkDupes and Fixmate Allow users to turn these off individually through configuration parameters May 23, 2012
Improved logging for Serial Executor Log capturing to same directories as used by cluster and halt on error May 23, 2012
Added Tools Type Tools are things that run within ASAP, such as ImportBam, GenerateBatch, etc. These no longer require RUN to execute May 24, 2012

-- EricTorstenson - 10 May 2012
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Topic revision: r9 - 27 Jun 2012, EricTorstenson
 

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