unicode quote characters embedded in it. These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset. Fixed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
a caveat: for anyone asking for all of the ROD's back from the RefMetaDataTracker (if your not using the facilities to get the track by name), you'll now be getting back a collection of GATKFeature objects. This object will contain the track name, and a method for getting the underlying object (getUnderlyingObject()), which will be the traditional RodVCF, rodDbSNP, etc. This layer is needed so we can integrate Tribble tracks (which don't natively have names). Calls that ask for RODs by name will still get back the traditional reference ordered data objects (RodVCF, rodDbSNP, etc).
Sorry for the inconvenience! More changes to come, but this is by far the largest (as has the greatest effect on end users).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3104 348d0f76-0448-11de-a6fe-93d51630548a
Introducing this into the pile of code which peeks under the covers of the SAMDataSource in the hopes
that this function can help to replace the others and provide a single path for crosstalk.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3103 348d0f76-0448-11de-a6fe-93d51630548a
of public interfaces. This won't be the last Picard patch, but it should be the last big one.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3096 348d0f76-0448-11de-a6fe-93d51630548a
Picard patch, including move of some of the Picard private classes we use to Picard public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3087 348d0f76-0448-11de-a6fe-93d51630548a
that bins will be present in the bin sparse array, which avoids the problem of having to hold the sparse bin array
stored in every BAM file index in memory at the same time.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3075 348d0f76-0448-11de-a6fe-93d51630548a
Results in drastic lowering of startup cost when multiple BAM files are
merged.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3066 348d0f76-0448-11de-a6fe-93d51630548a
ReferenceContext: constructor does not throw an excepion anymore when locus is not fully contained inside the window. So now we can have a reference context associated with a locus such that the window/actual bases do not cover the whole locus. Scary. I am not sure I like this...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3056 348d0f76-0448-11de-a6fe-93d51630548a
WARNING: If you update frequently, you might have to rm -rf ~/.ant/cache -- this is an unfortunate side effect of the way we
distribute picard-private.jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3050 348d0f76-0448-11de-a6fe-93d51630548a
meaning that in special cases of shallow coverage, an interval might get dropped.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2999 348d0f76-0448-11de-a6fe-93d51630548a
for test compatibility, but not sure whether we still need this feature. TODO: Poll the group about this feature.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2949 348d0f76-0448-11de-a6fe-93d51630548a
infrastructure can be torn down:
1) New sharding system emulates old MonolithicSharding mechanism.
2) Better awareness of differences between fasta and BAM files when creating
shards.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2948 348d0f76-0448-11de-a6fe-93d51630548a
awking output of BamToFastq vs. samtools until the outputs matched exactly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2945 348d0f76-0448-11de-a6fe-93d51630548a
GATK users from the readers, which they could abuse in ways that could destabilize the GATK.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2923 348d0f76-0448-11de-a6fe-93d51630548a
the mode of operation is currently queryOverlapping rather than queryContained.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2899 348d0f76-0448-11de-a6fe-93d51630548a
aaron
hanna
asivache