asivache
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9ec96414c7
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@114 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-20 15:54:29 +00:00 |
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asivache
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3565b50ff5
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main class (argument processing and traversing the reference) and implementation of all the Receiver functionality for building read piles over indels
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@112 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-20 05:18:04 +00:00 |
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asivache
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4c3b92b860
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comparator for interval objects
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@111 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-20 05:15:13 +00:00 |
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asivache
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4badd54216
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Indel also implements Interval interface but has its quirks
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@109 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-20 05:11:17 +00:00 |
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asivache
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29d2d460f3
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a trivial interface and even more trivial implementations that do nothing (ignore the data they receive)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@107 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-20 05:08:15 +00:00 |
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asivache
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875272e5c5
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moved counted object to utils
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@93 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-18 21:54:04 +00:00 |
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asivache
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708ada3e99
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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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@91 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-18 21:45:54 +00:00 |
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asivache
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37101045af
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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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@90 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-18 21:44:30 +00:00 |
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asivache
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151c37591e
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removed unnecessary import that produced a warning. where did it come from in the first place??
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@80 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-17 15:46:27 +00:00 |
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asivache
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36b8b34490
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Main tool that builds the clusters (multiple alignments) - so far; to be heavily refactored; most methods should find their proper homes in other classes
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@74 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-16 22:03:31 +00:00 |
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asivache
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b9ffcdf047
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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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@73 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-16 22:01:53 +00:00 |
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asivache
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a17ed3cbf1
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this class really computes (and keeps) a gapless pairwise alignment between the two sequences, ILT-style
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@72 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-16 21:59:26 +00:00 |
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asivache
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4972b03059
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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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@71 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-16 21:58:05 +00:00 |
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asivache
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6d481c64e7
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just a square matrix of arbitrary stuff; the stuff must be full fledged Java type, however, not a primitive type. Hooray Java!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@70 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-16 21:56:45 +00:00 |
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asivache
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c68e0cc1fe
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Walks along the sequence and emits a sequence of subsequent, encoded Kmers (uses short int, so currently it's up to K=8)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@68 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-16 21:54:45 +00:00 |
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asivache
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1e89dbfcb1
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Sequence bundled with its Kmer-based lookup index (same thing as old lookup table)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@66 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-16 21:52:57 +00:00 |