hanna f13d52e427 Attempt to determine whether underlying filesystem supports file locking and ... disable on-the-fly dict and fai generation. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3938 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-04 19:28:27 +00:00
..
features	Corrected location and made more explicit the error message thrown if someone tries to read a VCF 3.3 file with indels, which is not supported.	2010-07-29 20:02:47 +00:00
tracks	Attempt to determine whether underlying filesystem supports file locking and	2010-08-04 19:28:27 +00:00
utils	Added new query: isMNP(feature); returns true if dbsnp feature is multi-nucleotide polymorfism (e.g. a di-nuc TA ->CC)	2010-07-16 15:32:10 +00:00
BasicReferenceOrderedDatum.java	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +00:00
HapMapROD.java	Removed outdated Sequenom rod and renamed HapMapGenotypeROD to HapMapROD.	2010-04-11 01:43:07 +00:00
IntervalRod.java	major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.	2009-06-05 23:34:37 +00:00
IntervalRodIterator.java	Refactoring intervals, separating the process of parsing interval lists,	2010-04-13 15:50:38 +00:00
PlinkRod.java	No more new Allele() -- must use create. Allelel simple alleles are now cached for efficiency reasons. VCF4 codec optimizations -- 4x performance in general. Now working in general but hooked up to the ROD system now as VCF4. WARNING -- does not actually work with indels, genotype filters, etc.	2010-06-04 23:03:55 +00:00
RODRecordIterator.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
RODRecordListImpl.java	the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date.	2010-03-31 22:39:56 +00:00
ReadMetaDataTracker.java	the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date.	2010-03-31 22:39:56 +00:00
RefMetaDataTracker.java	Preliminary commit of new VCFCombine, soon to be called CombineVariants (next commit) that support merging any number of VCF files via a general VC merge routine that support prioritization and merging of samples! It's now possible to merge the pilot1/2/3 call sets into a single (monster) VCF taking genotypes from pilot2, then pilot3, then pilot1 as needed.	2010-06-30 20:13:03 +00:00
ReferenceOrderedData.java	the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date.	2010-03-31 22:39:56 +00:00
ReferenceOrderedDatum.java	Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files	2009-05-14 23:20:11 +00:00
SeekableRODIterator.java	fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.	2010-05-12 06:13:26 +00:00
TabularROD.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
Transcript.java	Transcript is now simply an interface	2009-09-23 18:13:31 +00:00
VariantContextAdaptors.java	1) When quals/GQs are really integers (x.00), strip off the floating points.	2010-07-20 18:01:45 +00:00
package-info.java	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00
rodGELI.java	adding VC adaptor for GELI, along with unit tests.	2010-04-23 05:28:39 +00:00