3e350006e0
Added a directory to house some Illumina output parsers. Hopefully this will be merged back into Picard at some point.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@126 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-21 17:55:56 +00:00
497eea2e5c
minor changes and shuffling code around; also, now when realigned piles are printed they are sorted by start position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@125 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-21 17:43:49 +00:00
1fcf4c0cbf
Update picard to work with new samtools.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@123 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 21:51:26 +00:00
5dca560c3c
A bunch of refactoring, and more on the way.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@122 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 21:31:07 +00:00
b806a9cf68
Updated for new version of samtools, which returns a sequence dictionary
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rather than a simple list of sequences.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@121 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 20:38:24 +00:00
c5433a3120
dumps out base qualities per position for use in making boxplots
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@119 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 17:01:18 +00:00
1161c261ac
made all data members public.
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switched logOddsVarRef to LOD.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@118 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 16:44:17 +00:00
f3f1b47808
deal with reverse complemented reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@115 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 16:01:49 +00:00
9ec96414c7
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@114 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 15:54:29 +00:00
3565b50ff5
main class (argument processing and traversing the reference) and implementation of all the Receiver functionality for building read piles over indels
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@112 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 05:18:04 +00:00
4c3b92b860
comparator for interval objects
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@111 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 05:15:13 +00:00
f810412d75
equals(), hashCode() updated/added, also a few minor changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@110 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 05:13:07 +00:00
4badd54216
Indel also implements Interval interface but has its quirks
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@109 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 05:11:17 +00:00
501e92d441
an interface for an interval object and simple minimum implementation; note: in contrast to arachne, this is closed interval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@108 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 05:09:56 +00:00
29d2d460f3
a trivial interface and even more trivial implementations that do nothing (ignore the data they receive)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@107 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 05:08:15 +00:00
6bcdac5c62
Restructured AlleleFrequency classes into 3 classes: AlleleFrequencyWalker, AlleleFrequencyMetricsWalker, AlleleFrequencyEstimate. AlleleFrequencyMetricsWalker class now calls mapper function of AlleleFrequencyWalker and works with the result. AlleleFrequencyEstimate is now a separate class instead of a subclass of AlleleFrequencyWalker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@102 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-19 22:06:01 +00:00
5fa99f430e
One line format is useable and two levels of debug output are available (debug = 1: one line format, debug = 2: table of sampled probs for each locus). Class AlleleFrequencyMetrics computes %dbSNP and frequency of SNPs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@99 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-19 15:05:05 +00:00
4242dba295
Remove endless iterator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@97 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 23:53:40 +00:00
225ea64bd9
Moved extra walkers at Mark's request.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@96 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 23:52:08 +00:00
ffb6f8f5da
Move the basic gatk framework into the core subtree.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@95 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 23:39:00 +00:00
69316f1873
removed unused import statement
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@94 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 21:56:15 +00:00
875272e5c5
moved counted object to utils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@93 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 21:54:04 +00:00
e09af2ef70
changed variable declaration from concrete class to interface
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@92 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 21:50:47 +00:00
708ada3e99
an accessory for CountedObject: builds a comparator for CountedObject<T> given a comparator for T; compares the underlying objects T themselves, *not* the associated counters
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@91 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 21:45:54 +00:00
37101045af
a simple wrapper class; less overhead than keeping a separate Integer counter object and going through object reallocation and/or autoboxing on each counter increment
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@90 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 21:44:30 +00:00
45d2a9acd8
Added walker to print out a histogram of where mismatches occur in alignments
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@89 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 19:46:42 +00:00
d46ee96269
Added support for loose Walker class files in walkers directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@87 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 17:32:24 +00:00
fe9e52c47e
allow on fly sorting AND validation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@86 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 15:50:17 +00:00
bb94c853f8
Added WalkerManager -- a class that dynamically loads available walkers
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from the jar file. For now, added placeholder Walker interface so that
WalkerManager could work with classes of type Walker rather than classes
of type Object.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@85 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 23:22:37 +00:00
d9fa04f65c
Fixed logic
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@84 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 22:20:03 +00:00
1aa3958644
Added ability to sort reads on the fly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@83 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 20:29:09 +00:00
0362cb9e59
added Utils.filterInPlace() - purges elements directly from the passed collection object without creating new list for results
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@82 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 19:06:40 +00:00
58aa2aab43
Rough draft of patch to use bam indices when available.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@81 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 16:39:03 +00:00
151c37591e
removed unnecessary import that produced a warning. where did it come from in the first place??
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@80 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 15:46:27 +00:00
478425b3d8
Better error messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@79 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 15:37:02 +00:00
0fd55d91d2
Fixed bug in unsafe mode
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@78 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 15:28:04 +00:00
c74bd871b1
added module for aligned reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@77 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 14:08:54 +00:00
28cc670a92
Walker to print out a histogram of aligned reads per mismatches allowed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@76 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 14:05:29 +00:00
9ae551e858
Lots of error checking added, fixed bugs associated with reading files out of order, added support for U (unsafe) flag for processing reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@75 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 23:22:04 +00:00
36b8b34490
Main tool that builds the clusters (multiple alignments) - so far; to be heavily refactored; most methods should find their proper homes in other classes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@74 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 22:03:31 +00:00
b9ffcdf047
matrix as the name suggests; utilizes special property (zeros at diagonal and below) to use less memory at the expense of slower access; this one is built directly on primitive data type (double) so it should not have any overhead associated with java classes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@73 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 22:01:53 +00:00
a17ed3cbf1
this class really computes (and keeps) a gapless pairwise alignment between the two sequences, ILT-style
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@72 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 21:59:26 +00:00
4972b03059
a class that keeps a pile of reads and can perform some simple computations on them; does not perform multiple alignments (so far) - external tools do the job
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@71 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 21:58:05 +00:00
6d481c64e7
just a square matrix of arbitrary stuff; the stuff must be full fledged Java type, however, not a primitive type. Hooray Java!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@70 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 21:56:45 +00:00
c68e0cc1fe
Walks along the sequence and emits a sequence of subsequent, encoded Kmers (uses short int, so currently it's up to K=8)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@68 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 21:54:45 +00:00
34d9af4702
Remove orphaned modules directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@67 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 21:53:05 +00:00
1e89dbfcb1
Sequence bundled with its Kmer-based lookup index (same thing as old lookup table)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@66 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 21:52:57 +00:00
685fc8bd61
Partial implementation of single sample allele calling
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@64 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 19:30:42 +00:00
8ccbcc4101
Mismatch counter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@62 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 15:51:48 +00:00
3b5003bd11
Added support for accessing the reference in read traversal
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@60 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 14:46:19 +00:00
kiran
asivache
hanna
jmaguire
ebanks
andrewk
depristo