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.
...
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
...
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
...
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
...
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
8f4bc8cb6e
Move filtering functionality into the PrintReadsWalker. More to come.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1010 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 16:38:08 +00:00
161c74716c
Forgot to change some direct references to variables in SSG. Fixed.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1009 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 14:16:18 +00:00
9eeb5f79d4
Various refactoring to achieve hapmap and dbsnp awareness, the ability to set pop-gen and secondary base priors from the command-line, and general code cleanup.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1008 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 07:21:08 +00:00
f2946fa3e8
Various refactoring to achieve hapmap and dbsnp awareness, the ability to set pop-gen and secondary base priors from the command-line, and general code cleanup.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1007 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 07:20:22 +00:00
f6af190b74
ignore clipped reads for realigning indel positions
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1006 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 01:01:27 +00:00
0583459839
Another formatting change to make Hapmap sites more clearly visible.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1004 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:53:21 +00:00
811f560efb
add refseq annotations to single sample calls
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1003 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:43:30 +00:00
e9be2a9c60
Changed a formatting issue.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1002 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:40:32 +00:00
ca09a10b76
refseq annotation rod is now manually bound to tell coding indels from non-coding ones
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1001 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:27:37 +00:00
5859948e80
Fixed bugs in CleanedReadInjector arising from integration testing.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@999 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 17:37:33 +00:00
fb7ba47fff
Now does really neightbor distance calculation, as well as true snp cluster counting
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@998 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 16:29:26 +00:00
dbf2cc037c
don't have a null-pointer hissy fit when the reference is N.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@997 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 13:59:16 +00:00
4eda040e0f
what used to be internal cutoff values are now exposed as cmdline parameters: minCoverage, minNormalCoverage, minFraction, minConsensusFraction
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@995 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 21:22:52 +00:00
41687d5237
Added accessors for the prior probabilities.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@994 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 21:16:10 +00:00
12dd18cdba
Now aware of Hapmap and dbSNP sites. We *can* change the priors there, but we don't yet.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@993 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 21:15:34 +00:00
d5cd883b99
bug fixed when a read with alignment end exactly at the window boundary and with last cigar element being an indel would cause index-out-of-bounds exception
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@992 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 21:03:15 +00:00
a12009e9e7
Added a new constructor in which priors for hom-ref, het, and hom-var can be specified. Otherwise, it uses the default values of 0.999, 1e-3, and 1e-5 respectively.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@991 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 20:33:45 +00:00
909fefa40a
Argumentized priors for hom-ref, het, and hom-var.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@990 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 20:32:44 +00:00
71e3825fa1
First pass of a walker for Eric that searches through an input BAM file for unclean reads, injecting the cleaned reads in their place and outputting the composite result.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@989 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 20:18:13 +00:00
032d0436e6
Added ROD for 1KG SNP calls
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@988 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 19:53:51 +00:00
ffffe3b2f6
-Support for 1KG SNP calls in RODs
...
-Minor bug fix
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@987 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 18:56:37 +00:00
63b5c12cbd
Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@985 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 18:13:22 +00:00
195b4ea7b4
a rename for consistancy of Sam to SAM, creating a genotype utils dir, and moving the GLF code into it.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@984 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 17:46:06 +00:00
599ceeddd8
Better method for downsampling deep regions
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@983 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 16:57:40 +00:00
4d9a88153a
Update inferred insert size of cleaned reads when they are paired
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@982 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 16:29:13 +00:00
3796654069
Added walker to emit intervals of clustered SNP calls
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@981 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 00:57:14 +00:00
678ddd914f
Stopgap fixes GFF, DbSNP being half-open rather than half-closed.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@980 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 21:38:57 +00:00
94b0e46d12
checked in a sample xml file used to store the defaults for the SomaticCoverage tool, and added it to the SomaticCoverage.jar in build.sml. Also added a inputStream marshalling method to the GATKArgumentCollection.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@979 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:46:16 +00:00
8d25f1a105
should be a little faster
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@978 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:33:45 +00:00
026f68fb41
a couple of quick name changes
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@976 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:02:52 +00:00
72a81f8f25
removed the requirement that a bam file list be present in the XML version of the command line arguments.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@975 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:01:13 +00:00
b1f90635c1
1. downsample when there are too many mismatching reads (needs perfecting)
...
2. allow user to specify that no reads be emitted
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@974 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 19:55:42 +00:00
39dcd4f11f
an attempt to bail out when unmapped reads are reached at the end of the file(s). still testing...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@973 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 19:53:50 +00:00
030efc468f
added naive ad-hoc cutoff for the pile size the cleaner will attempt to process; use --maxPileSize argument to force any pile larger than specified cutoff to be directly written to the output without cleaning
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@972 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:52:35 +00:00
f9be175f44
Be smart about trying alternate consenses:
...
try prior indels first and only 1 instance of them
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@971 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:43:22 +00:00
f304803811
initial check-in of an easy way to create command line tools based on the GATK
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@970 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:34:02 +00:00
b0cc763eb5
Added some methods to format bases such that read bases on the forward strand are in uppercase, while those on the negative strand are lowercase. This does *not* affect the default functionality of the standard PileupWalker
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@969 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:31:00 +00:00
9ebcd6546d
Convenience printing
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@968 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:07:38 +00:00
06e5a765f8
now has two modes: one sample - just call indel sites; two samples - call somatic-looking variants only. Still uses heuristic count-based cutoffs, cutoffs are hardcoded and are pretty conservative...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@967 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 16:41:38 +00:00
5451bbfd5a
-move final vars to command-line args
...
-Per Andrey: ignore indels from aligner when testing against alt consensus
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@966 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 16:39:00 +00:00
ad80894afa
Bumped picard to latest svn version.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@965 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 14:36:34 +00:00
ec2f015447
fixed a bunch of comments and license headers.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@964 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 14:10:46 +00:00
6bb7f7e9d8
Commented some stuff out so that things compile.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@963 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 14:06:33 +00:00
dc6a9ca196
Pooling resources to lower memory consumption.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@962 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 13:39:32 +00:00
87ba8b3451
Removed some useless code. Don't apply second-base test if the coverage is too high, since the binomial probs explode and return NaN or Infinite values.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@961 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 08:27:06 +00:00
a12ed404ce
Changed method name from applyFourBaseDistributionPrior to applySecondBaseDistributionPrior. 'Cause that's how I roll.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@960 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 08:21:22 +00:00
aaron
asivache
ebanks
kiran
hanna
depristo
jmaguire