Questionable jobs produced during DB rebuild |
When rebuilding a database where some files already exist, but there are missing files in early stages (such as alignment), ASAP will attempt to produce those aligned files, even though subsequent steps have already been recognized to be complete. |
Complete |
May 23, 2012 |
1.1.1 |
Add IMPORT function |
Users should be able to import BAM files that have already been aligned. Once imported, those files will work like bams that were created by one of the ASAP alignment steps |
Complete |
May 18, 2012 |
1.1.1 |
Add verify for executors |
This is necessary to catch invalid groups for PBS_ACCOUNT and GROUP_OWNER |
Complete |
May 23, 2012 |
1.1.1 |
Ignore Partitioned chroms missing from users chrom list |
Currently, if the user chooses to process only a subset of chromosomes, ASAP will attempt to realign, recalibrate etc over all of the partitions, even if those aren't requested. |
Complete |
May 23, 2012 |
1.1.1 |
Changing SUBREGION_SIZE can create issues with MOVE_BAM |
If the user generated scripts for one SUBREGION_SIZE and reran ASAP later with a different size, ASAP would look for all VCFs, even if the old ones can never be created except by manual execution. |
Complete |
Dec 03, 2012 |
1.1.4 |
Bam Summary |
Users can now use QPLOT to collect some thorough statistics for bams. |
Complete |
|
1.1.3 |
Moved template info into files for greater flexibility |
Template information resides in separate files which are dynamically loaded at runtime. This allows users to extend asap to some extent without needing to alter any pre-existing code |
Complete |
|
1.1.3 |
Split steps into steps and tools |
To differentiate commands like GENERATE_BATCH from CALL_SNPS, we have moved some functionality into tools. Tools must be specified on the commandline and run immediately. |
Complete |
|
1.1.3 |
Support for GATK2.x |
GATK 2.0 introduced a few changes in parameter names, so ASAP now allows users to switch default settings during configuration generation |
Complete |
|
1.1.3 |
Provide option to regular expressions |
ASAP now allows users to provide a comma separated file instead of regular expression for finding FASTQ and BAMs for GENERATE_BATCH and IMPORT_BAM |
Complete |
|
1.1.3 |
List tools beneath "available steps" during normal run |
Previously, users had to consult the manual to know how to spell tool names. Now, ASAP lists all available tools in the banner under the list of availalble steps. |
Complete |
Dec 04, 2012 |
1.1.4 |
List templates for all steps |
Added a tool, LIST_TEMPLATES, to iterate over each step and list all available templates. This is should make it easier to avoid mispelled template names. The search is live, so users who wish to create their own templates will be able to see those as well. |
Complete |
Dec 04, 2012 |
1.1.4 |
List templates for active steps |
Optional templates are listed beside each "Active Step" in the banner. |
Complete |
Dec 04, 2012 |
1.1.4 |
WGA alignments run out of time unless TIME_CALIBRATION is set very high |
Added a new setting to GENERATE_BATCH that allows the user to "calibrate" the alignment time. We recommend setting this to 6.0 for WGA alignments. |
Complete |
Dec 05, 2012 |
1.1.4 |
SNP calls are generated even if no bams exist |
An error has been fixed that allowed the variant caller steps to produce scripts even if there is no available BAMs connecting to it. ASAP now reports that no scripts were produced and attempts to explain the possible reasons for this (it's not always an error). |
Complete |
Dec 05, 2012 |
1.1.4 |
BAMS can be imported when chromosome appears in dir name |
Previous, the regular expressions ignored the directory structure. ASAP now allows regular expressions to capture sample/chromosome information from the directory structure as well as filenames (if written correctly) |
Complete |
Dec 05, 2012 |
1.1.4 |
Samtools halts during recalibration in Serial Mode |
If the variable, KEEP_TEMPORARY_FILES is set to true, samtools will fail on a merge due to the presence of merged.bam. I have changed samtools to force the output of the file and added a line to delete the file when it is no longer used |
Complete |
Dec 12, 2012 |
1.1.5 |
Completion of Recalibration deleted file from realignment under certain circumstances |
This bug was introduced as a fix to serial execution KEEP_TEMPORARY_FILES. Recalibration was deleting files from the realignment directory upon completion if there was no need to merge multiple files. This didn't affect downstream progress, however, if is unintended behavior. |
Complete |
Dec 19, 2012 |
1.1.6 |
Issues exist when the user deletes data from the "intermediate" steps before ASAP can identify they were completed |
When run in Serial Mode, ASAP doesn't use tokens and job IDs. So, it has no way to recognize that a job was completed successfully except for the presence of output. If the user deletes intermediate data, say for realignment before rerunning ASAP to catalog it's completion, it will iterate down to realignment, see that no data is there, generate scripts before stepping up to Recalibration and recognizing that those data are there. In this case, halting the serial execution and rerunning it will behave correctly (the recalibration will find it's data is completed before pushing back to realignment). However, it is possible that unnecessary computation will be expended in these cases. |
In Progress |
|
|