c4d9058f32
Added module rodVariants.class to the list of allowable RODs.
...
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.
...
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.
...
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...
...
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.
...
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.
...
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.
...
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
...
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
...
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
...
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
...
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
...
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.
...
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.
...
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!
...
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
...
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
...
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 (?)
...
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.
...
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.
...
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
kiran
kcibul
aaron
hanna
depristo
jmaguire
asivache
ebanks