f20cdbe60a
Modified to work with MT containing VCFs.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3910 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-30 14:59:59 +00:00
6d91cd587e
Be explicitly clear about which options are for debugging purposes only and shouldn't be used if your username is not ebanks@broad. If only we had a @hidden annotation option for args...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3909 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-30 14:18:31 +00:00
ac8048f17b
Support for automated selects for tranches in variant eval -- use -tf to make tranch-specific ve outputs. ApplyVariantCuts with tranche reading functions for general use, along with todo for ryan. CombineVariants now has --filteredAreUncalled and will treat filtered snps in input VCFs are uncalled, and so won't emit -filteredInOther set features
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3908 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-30 14:16:43 +00:00
9231d13252
Minor modification: adding an argument to make slightly more general.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3907 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-30 05:20:20 +00:00
db54d63fc7
Hahaha yes, ownage. This now works.
...
BTW, Eric, thanks for forwarding the DepthOfCoverage thread to gsamembers. I'd forgotten about reduce by interval. Mighty helpful in this case!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3906 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-30 04:23:02 +00:00
3e3f8c7692
Simple count intervals walker, as per my recent email to GSAMembers. Never use this. It doesn't behave the way you think it does.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3905 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-30 03:39:23 +00:00
9132c98eec
Slightly smarter interval list dealing (whole exome intervals are .interval_list, whole genome are .interval.list). Also use BTI with the Genomic Annotator
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3904 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 22:04:02 +00:00
54d93f63d2
Hacky fix for LSF confusion -- submitted jobs check to see if their directory exists, despite depending on the job which creates said directory. Filter strings now have escaped quotes.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3903 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 21:35:50 +00:00
0f9baa2e94
Ha ha ha ha ha
...
:(
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3902 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 20:48:35 +00:00
ba1a330293
Corrected location and made more explicit the error message thrown if someone tries to read a VCF 3.3 file with indels, which is not supported.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3901 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 20:02:47 +00:00
735ef19dc8
Added option to sleep after creating temporary directories.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3900 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 19:53:17 +00:00
82c37fceb5
Create intermediate directories and don't error if the directory already exists.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3899 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 19:45:12 +00:00
7a5ee485d2
Full pipeline now works through DAG creation. First draft; more work to do to make it cleaner and better command-line input handling (and properties handling); but the DAG is rendered and looks good.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3898 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 19:36:17 +00:00
5af986e0c1
Add an integration test for Beagle (one for ProduceBeagleInput and one for BeagleOutputToVCFWalker)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3897 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 18:49:22 +00:00
4d4cf6e1dc
Updates to calling pipeline
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3896 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 18:37:20 +00:00
52f24c86fa
Script to split a provided interval list into contigs. Excesses will be dropped into the last provided file. Works like splitIntervals.sh. This is for Queue.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3895 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 16:42:53 +00:00
62a9217a61
A brute-force exome/genome independent end-to-end cleaning/calling pipeline using Queue
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3894 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 13:17:14 +00:00
f35e6d73b4
Actually name the class the name of the file. (Clearly created by cp)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3892 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-28 15:18:04 +00:00
cd9395fa14
Since Picard's FixMateInformation merges, fixes mates, and sorts, allow it to be used as a gather function.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3891 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-28 15:09:19 +00:00
e1a34685fd
Add back MyHaplotypeScore as a new implementation for HaplotypeScore, this time as a non-standard annotation. Implementaiton is also better, it computes better consensus haplotypes, ranks them by sum of quality score.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3890 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 21:23:19 +00:00
6c93b13428
A Java sizeof, implemented using the Java instrumentation API. Can either get the memory consumed either only by a single
...
object or by a single object and all the references it contains. Requires a command-line change to add a Java agent to
the command-line; see the Sizeof.java javadoc for details.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3889 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 18:44:15 +00:00
f5566a6593
Knocking out some quick findBugs.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3887 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 14:10:59 +00:00
894623858d
OK, bad idea to add new temporary annotation - revert to keep integration tests hapy.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3886 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 12:07:13 +00:00
71bfb1ee35
First redesign of HaplotypeScore - now, a different approach is taken to build possible haplotypes at a site: first, all possible haplotypes consistent with reads are formed (reference is not used). After this list has been formed, it is ranked according to the number of reads that are consistent with it and the two most popular haplotypes are chosen.
...
this reduces to the old method in typical cases, but it builds haplotypes correctly if there are two variants close by within a context window.
Annotation is temporarily named MyHaplotypeScore so it can be run in parallel with old one, soon it will be renamed after some more testing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3885 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 10:54:56 +00:00
cffebcc867
Small utility walker used for production of the Beagle data processing paper section. Walker will print out to output file, for every site common to a reference vcf and an eval vcf, a given sample's depth, hapmap AC and AF and pre/post Beagle genotype as well as corresponding reference (e.g. Hapmap) genotype.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3884 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 03:00:17 +00:00
1d9ed1e214
Cleanup of old VCFRecord code
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3883 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 02:56:47 +00:00
7dd55fbf13
Archiving
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3882 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-27 02:47:18 +00:00
9667942e52
fix for Ryan's issue: we also need to sync when we store a resource.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3881 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-26 22:17:47 +00:00
8b072b59e2
Returning index dumping functionality in BAMFileStat to a useable state.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3880 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-26 20:03:50 +00:00
19ad44d332
Minor improvements to CombineVariants to handle the complex case from Chris. IntegrationTest of complex case.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3876 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-25 13:46:11 +00:00
7c5a3836db
Trivial changes
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3875 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-25 04:00:47 +00:00
56de475f11
Based on feedback from non-GSA users, who claim that our exceptions are 'scary and overwhelming,' I've cleaned up the error message to first describe the error and what users should do and then ask them to copy the subsequent stack trace into their GetSatisfaction posting.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3874 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-25 03:57:44 +00:00
9bd8a2685b
Because the performance tests were busted on LSF, no one caught this error until now: when Matt changed over the contract for the AlignmentContext, this line needed to get updated too. All is well now.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3873 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-25 02:53:01 +00:00
b551eaf8fd
Actually commit the code that makes variant eval run in a reasonable amount of time.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3872 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-24 17:32:03 +00:00
b0b37c3476
No handles (I believe) reference only VCs correctly
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3871 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 23:09:23 +00:00
e21376219d
Updates to CombineVariants for Tim. -setKey can be null. Integrationtests for -setKey foo and -setKey null.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3870 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 22:35:52 +00:00
26bb1cd9ce
Fix broken test correctly
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3869 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 20:47:41 +00:00
4fc1db7aaf
Change interface to VCFWriter add() method to take only 1 byte from reference (since that's the only thing it needs), to prevent bugs like having people call it with ref.addBases() which is wrong (since it provides bases starting from the left of reference context window).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3868 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 20:24:03 +00:00
b3fd145161
fix for a bug deep in the tribble indexing: if you had a single record in the first contig, the second contig's index blocks would point to the wrong file seek location, and you'd see no
...
features in that contig. Thanks to Mark for finding this. I'm not rev'ing the index version (which would cause all indexes to be rebuilt), since this seems like a pretty rare edge case.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3865 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 18:39:55 +00:00
33090629ea
VariantEval can now see the EvaluationContext group objects, so they can decide if/when to print interesting sites. GenotypeConcordance has a hard-coded option to print FNs that is on the way to being generally useful. VCFWriter now uses the US locale for formatting floating point numbers; I believe this fixes a long-standing annoyance. Italian guys will check on this.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3864 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 17:16:50 +00:00
77cace3aff
It's probably a good idea to look carefully at what you've done before actually committing
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3863 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 17:06:54 +00:00
44f9a631d6
Adding CombineVariants to release. Pining for the days when all of core/playground will be part of release by default...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3862 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 16:53:18 +00:00
5eef15cfdf
a) Bad bug fix to CombineVariants: when indels were being merged, the reference base provided was wrong - ref.getBases()[0] was being used, but this returns bease at start of window. Instead, the reference at current locus should be used.
...
b) Cosmetic change to Beagle annotation description.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3861 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 15:13:47 +00:00
4ff8b8fc0e
1. Fixing a bug that Mark found where indel-containing clipped reads would get an original cigar tag even when they didn't actually get modified.
...
2. Added some useful logging messages.
3. Added a oneoffs walker to calculate the number of realigned reads and intervals containing them.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3860 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 14:24:01 +00:00
973934f769
Depth of coverage now uses longs rather than ints. We can now successfully run on the Lepidosiren paradoxa genome. (about 80 GB)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3859 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 14:14:12 +00:00
536399eaa0
Improvements to variant combine. Now calculates AC/AN/AF correctly by calling into the VariantAnnotator engine. Automatically removes annotations that are inconsistent across incoming VCs (in simpleMerge). TODO bug fix for Guillermo/Eric.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3858 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 13:33:11 +00:00
9579aace1f
updates to code dependent on Tribble, as well as the following Tribble changes:
...
- makes writing to disk optional for indexes using the indexCreator classes (allow the user to specify the index file, if null don't write it)
- removed some system.out debugging code
- fixed version checking in interval tree
- made indexes store and return a LinkedHashSet for sequence names (to ensure they've preserved the ordering in the file)
- index creators now read the file before creating the index
- changed the Index.write() method to take a LEDataStream instead of a file
- removed the sequence dictionary code on the header
- added utils for getting LEDataStreams
- added a base Tribble exception
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3857 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 01:56:10 +00:00
c5325b03be
1) Removed hard-coded strings. Please let's use the fields defined in VCFConstants.
...
2) General code cleanup.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3856 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 01:49:47 +00:00
e9d243babb
More improvements to exception handling during multithreaded runs based on
...
a bug reported by Ryan.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3855 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-22 22:13:01 +00:00
83798225ac
Repackaged datasource-specific command-line tools into their own package. Added a tag renamer tool.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3854 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-22 19:50:34 +00:00
chartl
ebanks
depristo
delangel
kshakir
hanna
rpoplin
aaron