bfbf75fe3e
Fix error in command-line validation: don't ever allow intervaled access to unindexed read stream, no
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matter what type of traversal it is.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4997 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-14 02:49:04 +00:00
00310c05bb
Fix corner condition that happens when there are indels right at the end of a contig and there's not enough reference to build a haplotype.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4996 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 21:08:22 +00:00
c0031b05ff
Stamp out lazy loading in the PluginManager. This is an attempt to stamp
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out the non-deterministic VariantEvalIntegrationTest errors we've been seeing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4995 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 20:58:28 +00:00
2163420942
Updated to reflect QD changes in r4984
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4994 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 20:10:21 +00:00
02dc0f97d1
Remove testWalkerUnitTest; it doesn't actually do anything and just adds
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extra cruft to the output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4993 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 19:02:00 +00:00
c4f9b262e5
removing the tech dev pipeline script from the repository to keep the methods development pipeline as the reference script.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4992 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 18:15:55 +00:00
b107c97c1a
Cannot have "=" sign in reason, so change to ":"
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4991 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 17:23:44 +00:00
b4a2112a0d
Added the "previous locus" to interesting sites VCF (locus with respect to which the site is phased)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4990 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 17:19:20 +00:00
e8f0ae4b09
Renamed and documented some phasing-specific classes to make their purpose clearer to someone browing through the code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4989 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 16:17:36 +00:00
6b5474a00a
This updates the script to produce a more tearsheet-like output for sample set statistics. Formatting will be updated for aesthetic improvements. There are also several database options that currently pull out misleading information because of changes in sequencing methodology that will be updated to show correct information. Eventually, plot formatting will be updated as well and additional informative plots will be added.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4988 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 15:59:06 +00:00
ffae7bf537
Moved phasing-specific utilities to phasing sub-directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4987 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 15:38:20 +00:00
91824f478e
FASTQ directory is gone
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4986 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 15:16:06 +00:00
e3956148ac
removing unused fastqtobam
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4985 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 14:29:32 +00:00
ce3d226183
Reverting back to the old definition of QD because it works better with large numbers of samples. The new QD is relegated to a new annotation: sumGLbyD. Tweaks to the new HaplotypeScore based on evaluation with better QD calculation. The default qual threshold in GenerateVariantClusters is updated to be in line with the variant quality scores coming from the exact model.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4984 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 14:12:30 +00:00
e0092bb160
Experimental feature: change the rate at which log messages appear on-the-fly
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and enable/disable performance logs from outside the JVM process. Making this
available for the moment; we'll see whether it ends up being useful.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4983 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 04:20:53 +00:00
9e93091e9a
-baqGOP now takes phred scaled scores instead of probabilities in the command line.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4982 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 00:06:38 +00:00
5736d2e2bb
Something I should have done a long time ago: attempt to detect whitespace
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after the line continuation backslash and enhance the error message if it
appears.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4981 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 23:15:08 +00:00
edebbb5aa0
Fixed long-standing bug reported by Mauricio where @Arguments assigned to
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primitive types were properly validated and throw the proper
MissingArgumentValue UserException. Before this fix, the error reported
was the infamous DePristo BSOD (Could not create module String because
an exception of type NullPointerException occurred caused by exception null).
Thanks Mauricio!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4980 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 22:18:24 +00:00
6d855041ec
Oops...forgot to commit the changes that allow primitive VCF streaming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4979 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 21:54:51 +00:00
8a6b126ea8
Several cleanups to IndelMetricsByAC:
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- No longer a standard eval module to keep integration tests happy
- Remove class name overlaps with SimpleMetricsByAC so that modules don't overwrite each other's files, and to make it easier to grep results.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4978 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 18:35:24 +00:00
8fe5641b2e
can explicitly set the now required ReferenceDataSource in unit tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4977 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 18:25:12 +00:00
7916ab0ed5
remove the index each run
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4976 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 17:38:22 +00:00
468ef382b7
vastly improved progress meter that estimates % of work done and time until the job finishes and time remaining. Reordered GATK core initialization order -- intervals are created before the scheduler.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4975 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 17:32:27 +00:00
bdd382198c
Necessary changes to enable HaplotypeScore annotation for indels
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4974 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 01:09:12 +00:00
23597a2bde
Variant Eval module that collects indel statistics (basic counts and event sizes) and partitions by AC (similar to SimpleMetricsByAC in the SNP case)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4973 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 01:08:09 +00:00
48052907a6
A hom genotype can always be considered phased
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4972 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-11 18:48:48 +00:00
c2dd956888
Moved PrintReferenceVariantsWalker to playground
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4971 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 22:07:41 +00:00
8ba3a5a43f
Command lines for locally run Queue jobs no longer have to be escaped differently than bsub'ed jobs.
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GSA-410 Local job runs now can run command lines longer than than 4096 on our linux machines.
When determining if the help text and Queue extensions need to be rebuilt, use the .class files not the .java so that GATK oneoffs are picked up correctly.
Added the most basic of all example QScripts for debugging, Hello World.
Minor updates to copy/pasted LSF code to reduce ant javadoc warnings by a third.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4970 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 21:07:29 +00:00
ee348ac9d4
Add a hidden mode to the realigner to turn off SW but still use indels other than known ones (i.e. those already in the reads)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4969 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 20:27:04 +00:00
01c2091cd9
A LocusWalker to print the haploid reference genome as a VCF file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4968 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 16:59:41 +00:00
9648399630
Boneheaded silly bug in indel caller - posterior probability computation was using priors gotten from SNP heterozygosity, not indel heterozygosity. Added then indel het. argument to command line and hook it up (not a radical change in calls though, just a few dubious calls around the edges fall off)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4967 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 14:56:28 +00:00
0e089ce0b7
watch -n 30 shell/pipelineJobs.csh for those who want to watch the gsaadm's jobs progress
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4966 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-09 13:09:30 +00:00
298dce2940
Adding the native jna support libraries from the jna.jar to the Queue package jar.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4965 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-08 10:48:30 +00:00
b24e1134f9
unfortunately samrecord pileup also uses zero length intervals to indicate deletions; this will have to be a BED specific exception.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4964 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 22:32:50 +00:00
b34e2f733f
Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.
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Updated the Queue scatter/gather for read walkers to include -L unmapped on the last scatter job when intervals aren't specified, and to map it correctly when it is explicitly set.
Simplified the build.xml/ivy.xml to fix a bug reported with "ant clean dist test" where the scalac target wasn't found.
Now building all scala code at the same time, just like all java code is compiled at the same time.
Sped up the build for everyone by uncommenting a small bit of classes so that javac/scalac will not constantly launch trying to build .class files that will never compile.
Moved some source files to their expected location so that the .java/.scala -> .class is a one-to-one match, again keeping the compilers from wasting cycles.
Used <uptodate> and <touch> to skip extracting the help text and generating the GATK Queue extensions when the source files haven't been modified.
Fixed a couple errors when the <javadoc> task is run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4963 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 22:03:36 +00:00
be67161b47
Deleting old shell code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4962 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 21:36:16 +00:00
e64a300642
Deleting old python code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4961 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 21:33:45 +00:00
3362f0c280
Private mutation simulator and analysis routines for EOMI paper
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4960 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 21:23:29 +00:00
60f45a7c49
Stupid me. Forgot to put this check in the last commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4959 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 19:16:41 +00:00
56b87da8f9
a better error message for the situation where a RMD track generates a negitive length interval; the user will now see a message like "Bad input: A feature produced by the reference metadata track named "bed" at position chr1:10434-10433 has a start greater than the stop; this is an invalid position "
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4958 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 19:06:04 +00:00
4272b824d6
unused imports
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4957 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 18:33:12 +00:00
3e7802a3e0
Minor changes to a qscript and the GQ constants on PrivatePermutations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4956 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 18:26:21 +00:00
79fcff13ff
Fixed import statement that was erroneously referring to VE3 rather than VE2.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4955 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 03:22:25 +00:00
f3ca2cc9de
Add safety net to BAQ calculation: explicitly cast to byte/int and check for bad values
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4954 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 18:09:12 +00:00
2ac5c52281
Better error message as per Mark
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4953 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:44:02 +00:00
e0d091b3db
Die gracefully if the bam is malformed with quals that are too high
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4952 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:39:08 +00:00
3163970ad5
Updates that slipped from my last commit: fixed some imports and calls to super().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4951 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:34:40 +00:00
3b76034d50
Namespace changes to avoid conflicts with other packages.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4950 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:33:26 +00:00
ab143c82af
Selects only the project requested via the Oracle command, rather than selecting everything and then subsetting.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4949 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:32:32 +00:00
d88fd7212f
Changes to allow the primary key of a table to be hidden. Formatting changes to account for when that column is hidden.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4948 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:27:19 +00:00
hanna
delangel
kshakir
carneiro
fromer
corin
depristo
rpoplin
aaron
ebanks
chartl
kiran