bin tree are dictated by the lowest bin level, whether it exists or not.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5339 348d0f76-0448-11de-a6fe-93d51630548a
an unexpectedly small amount of data is present.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5338 348d0f76-0448-11de-a6fe-93d51630548a
optimizer was mutating the data stored in the indices. Protosharding still
disabled by default.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5334 348d0f76-0448-11de-a6fe-93d51630548a
- No more duplicate intervals
- Truncation at intervals that already exist, e.g.
exists: |--------| |-------|
new: |---------|
fixed: |-----|
note that weird instances like:
exists: |-| |-| |-|
new: |---------------------|
fixed: |----|
e.g. you're truncated to the nearest interval on whatever side. In general many behaviors could happen in this instance, this is the one currently implemented.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5323 348d0f76-0448-11de-a6fe-93d51630548a
mdcp: Some class structural changes due to the inclusion of indel calls. ApplyCut now chooses the tranche differently for each dataset.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5319 348d0f76-0448-11de-a6fe-93d51630548a
Using the name of the yaml in the log file name instead of each writing each to "queue.out" so that two yamls can run from the same directory without creating cycles in the graph.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5318 348d0f76-0448-11de-a6fe-93d51630548a
are works in progress, and this checkin will provide a baseline against which to gauge
improvements to both projects.
Low-memory BAM protoshards (disabled by default):
- Currently passing ValidatingPileupIntegrationTest.
- Gets progressively slower throughout the traversal, but should run at least as fast as original implementation.
- Uses 10+ file handles per BAM, but should use 3.
BAM performance microbenchmark test system:
- Currently tests performance of BAM reading using SAM-JDK vs. GATK
- Tests do not hit all GATK performance hotspots.
- New tests that require input data in a slightly different form are hard to implement.
- Output of test results is not easily parseable (investigating Google Caliper for possible improvements).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5317 348d0f76-0448-11de-a6fe-93d51630548a
- a LOT more error reporting to stderr and exit codes
- split the firehose pull down into a TSV generators and a TSV to YAML converter
- YAML converter is compatible with the TSVs generated by the front end website and will grab only the appropriate columns
- deprecated getFirehosePipelineYaml.sh mode with a single Sample_Set name which uses the Firehose test harness
- new getFirehosePipelineYamle.sh mode using web services API and requires an additional parameter, a password config file with "-u <user>:<pass>" which has been tested on problematic Sample_Sets
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5313 348d0f76-0448-11de-a6fe-93d51630548a
directory updates in the methods pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5305 348d0f76-0448-11de-a6fe-93d51630548a
Small fixes on the data processing pipeline
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5304 348d0f76-0448-11de-a6fe-93d51630548a
BatchMerge - additional support for indels (can't just test the alternate allele when it's an extended event, must also specify that you want to use the dindel model when you actually test the allele)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5300 348d0f76-0448-11de-a6fe-93d51630548a
TODO: Switch to bulk status checks and add status archive lookups.
Sending SIGTERM(15) instead of SIGKILL(9) to allow for graceful termination of child process.
Printing out the name of the QScripts in the compile error text.
Added a pipelineretry -PR pass through for the MFCP and MFCPTest.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5295 348d0f76-0448-11de-a6fe-93d51630548a
ExpandIntervals now checks that identical intervals are not created by (un)fortunately-spaced targets
VCFExtractIntervals no longer creates duplicate intervals in the case where a VCF has multiple entries at the same site
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5294 348d0f76-0448-11de-a6fe-93d51630548a
hanna
chartl
ebanks
carneiro
delangel
depristo
kshakir
kcibul
rpoplin
asivache