26eb362f52
Added novel / known split to variant eval. That is, emits all of the standard analyses on SNP partitioned into those known in the provided known db and those novel. Also fixed problem with counting bases within subsets
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1068 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-21 21:27:40 +00:00
d3f0c51944
longer update times so we don't overwhelm when running genome-wide
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1067 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-21 14:10:02 +00:00
a21c2a7e48
don't make mapping quality too high
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1066 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-21 04:51:42 +00:00
686c8133ed
massive change in the way the cleaner works, mostly revolving around the fact
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that we no longer trust indels from the alignments (although we do use it as
a good alternate consensus possibility).
Other changes include better "greedy mode" performance and allowing the user
to have just the cleaned reads themselves be printed out (mostly for Matt's
CleanedReadInjector).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1065 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-21 03:56:59 +00:00
9e26550b0d
Apprach v2. Added python analysis script, so java no longer must be used to analyses quality score data. About to refactor out lots of unneeded code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1063 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-20 16:00:23 +00:00
dde52e33eb
Cleanup of the cleaned read injector based on Eric's feedback.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1062 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 22:04:47 +00:00
a0a3cf2f9f
VariantFiltrationWalker can now apply specified exclusion tests after the feature tests. For a given variant, all reasons for exclusions are printed to screen.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1061 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 21:12:01 +00:00
8ac40e8e2d
Updated version of the recalibration tool
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 17:45:47 +00:00
aef519b427
more comparisons
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1059 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 16:46:05 +00:00
58b132ee10
Eliminate redundant computation.
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Still room for more optimization, but I called chr20 (60Mb) in a couple hours on the queue this morning.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1058 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 16:31:57 +00:00
3a1b58ca65
remove unused argument lodThreshold.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1057 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 12:40:12 +00:00
9a0151b7e1
Added an option to list all available feature classes and exit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1056 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 00:00:12 +00:00
ed7afd8b70
Added javadocs. Now throws an exception if an unknown feature is specified. General cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1055 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 23:28:38 +00:00
284fd6a5fb
VariantFiltrationWalker now inspects its parent package and determines the list of features that can be applied. Command-line specification of filters to run look at the simple names of these features and do a case-insensitive match to determine which features to apply. A new verbose mode allows the user to see how the likelihoods are changing with the application of each subsequent feature.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1054 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 22:45:36 +00:00
0a0ef573f7
Methods for finding classes given a path and finding classes that implement a given interface. This stuff was mostly copied from private methods in WalkerManager, so there's some code redundancy. At some point, those calls could be replaced with these.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1053 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 22:43:19 +00:00
d748c85dc4
Cleaned code and reorganized -- moving in the right direction for v2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1052 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 22:28:34 +00:00
af7a759ba4
Convert the somatic coverage tool to output from the packaging tool rather than from the dist target.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1050 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:29:30 +00:00
1bca144119
Moving things around
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1049 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:06:46 +00:00
ca8a3bd85e
Another temp checking for rearranging things
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1048 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:04:36 +00:00
3c40db260d
Added REFERENCE_BASES required annotation for performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1047 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:03:57 +00:00
03fe166994
Wrote a public static version of loadFirstNReasonableReadsTrainingSet() so Alec can call it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1046 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 20:18:17 +00:00
a4fa02f11c
Moved output outside of for loop so I don't have 10 different versions of the same variant (though, now that I think of it, that's not necessarily a terrible thing for debugging...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1045 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 19:59:26 +00:00
768a16e791
An experimental, tile-parallel version of the secondary base annotator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1044 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 19:58:09 +00:00
e26df45e8e
Different features can now be specified by repeatedly supplying the -F "featurename:arguments" option.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1043 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 18:45:03 +00:00
7a921c908c
Can now adjust the genotype likelihoods of a variant returned from the rod. This automatically causes the lodBtr, lodBtnb, and genotype to be recomputed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1041 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 07:26:37 +00:00
9a7cec7d2e
Directory to house variant calling and filtration tools.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1040 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 07:20:38 +00:00
5992d88409
skip N's in the reference (rather than crash. doh!)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1039 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 23:22:35 +00:00
c4d9058f32
Added module rodVariants.class to the list of allowable RODs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1037 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 21:33:13 +00:00
ab2a80f3ea
A new ROD type that allows one to input a geli.calls file back into a walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1036 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 21:32:21 +00:00
9ef391706c
Added outputting of genotype posteriors to geli.calls file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1035 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 21:31:46 +00:00
615572ea06
output to out... not System.out...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1034 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 20:43:10 +00:00
b947fd586f
FIxed a nasty bug in GenomeLoc compareContigs; we were using '==' to compare Integer contig ID's. The surprising thing is that it actually works for Integers > -127 and < 128 (they're cached by the JVM, so it's actually comparing the underlying ints). Switched over GenomeLoc contigs to int based.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1033 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 20:19:47 +00:00
cba9025983
More package-level documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1030 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 16:28:45 +00:00
43a28750e0
Package level documentation -- helps new users get acclimated to the codebase more quickly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1029 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 16:27:48 +00:00
673205ed5f
additional output tweaking
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1028 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 15:37:38 +00:00
7d281296a7
Finishing checking for building
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1027 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 14:12:40 +00:00
d1e25bfe88
Intermediate checkin for safety -- now compiles
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1026 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 13:16:55 +00:00
2250769a42
Intermediate checkin for safety -- do not use
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1025 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 13:07:19 +00:00
86c8c08375
Intermediate checkin for safety -- do not use
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1024 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 13:06:24 +00:00
78b7fb25c7
allow contig names to have spaces in the fai. This is not yet supported by samtools fai generator (which truncates at the first space), but we might as well fix it on our side.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1022 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 22:23:12 +00:00
6ee64c7e43
added changes to support alec toUnmappedRead seek. Huge improvements (orders of magnitude) in unmapped read performance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1021 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 22:15:56 +00:00
4f6d26849f
Behold MultiSampleCaller!
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Complete re-write of PoolCaller algorithm, now basically beta quality code.
Improvements over PoolCaller include:
- more correct strand test
- fractional counts from genotypes (which means no individual lod threshold needed)
- signifigantly cleaner code; first beta-quality code I've written since BaitDesigner so long ago.
- faster, less likely to crash!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1020 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 20:03:24 +00:00
7db4497013
fixing the readTraversal output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1019 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 19:44:38 +00:00
b11c5a7cd5
doing some read validation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1018 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 19:25:43 +00:00
010304fe44
bug: printing incorrect coordinates into output, finally fixed (?)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1017 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 18:08:56 +00:00
647b8a1ab0
Fix TabularROD printing and testing so Aaron stops nagging me.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1016 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 15:49:26 +00:00
a0a549557f
added a check of the sort ordering to the query methods, so that we detect if a file is unsorted much earlier. Also added some verbosity to the exception; it now contains an information about the raw attribute we saw for 'SO', the sort order of the bam file.
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Also fixed a bunch of documentation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1015 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 22:15:03 +00:00
2259dc3a8f
added filtering out indels with large levels of noise (mismatches) remaining in the close proximity; also a bug in recording deletion coordinates is fixed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1014 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 21:13:28 +00:00
a6477df6d1
Now optionally outputs whether "SNPs" are maintained/cleaned out/introduced by cleaning
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1013 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 20:02:02 +00:00
11aa715630
added capability for filtering by platform
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1011 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 19:19:50 +00:00
depristo
ebanks
hanna
kiran
jmaguire
kcibul
aaron
asivache