Build javadoc for variant and tribble packages as part of sourceforge release.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1656 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix spelling error in TestUtil method.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1657 8bce386e-0d6e-43e0-b1ca-608082c0432d
sam-jdk must compile before tribble

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1658 8bce386e-0d6e-43e0-b1ca-608082c0432d
Refactored MathUtil.max() into a method that returns the index of the max value and had max() call that method.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1659 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix annoying bug where in order to use SamLocusIterator as an iterator one first had to call the .iterator() method on it to prime it.  Now auto-primes.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1660 8bce386e-0d6e-43e0-b1ca-608082c0432d
Changed to call SAMFileReader(File) instead of SAMFileReader(InputStream) so that SAMFileReader can use the knowledge that it's reading a file.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1661 8bce386e-0d6e-43e0-b1ca-608082c0432d
Support writing of vcf.gz, but only without on-the-fly index creation.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1662 8bce386e-0d6e-43e0-b1ca-608082c0432d
Set buffer size of BclReader to Defaults.BUFFER_SIZE, which defaults to 128K and can be controlled via -Dsamjdk.buffer_size=<buffer_size>.  Previous size was always 8192.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1663 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added nominal support for VCF4.2 headers (but just the headers)

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1664 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.107

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1665 8bce386e-0d6e-43e0-b1ca-608082c0432d
Enable async I/O for writing bgzipped VCFs



git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1668 8bce386e-0d6e-43e0-b1ca-608082c0432d
Mark library as not requiring executable stack

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1669 8bce386e-0d6e-43e0-b1ca-608082c0432d
Improved MarkIlluminaAdapters to handle files with mixes of paired-end and single-end reads, clip for multiple different adapter sequences in one pass and correct progress logging and metrics that were only counting one read out of each pair.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1670 8bce386e-0d6e-43e0-b1ca-608082c0432d
Minor change so that VCFFileReader.getSequenceDictionary() does not require the VCF to be indexed.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1671 8bce386e-0d6e-43e0-b1ca-608082c0432d
Changed the way IoUtil.unrollFiles() works to a) work with compound extension (.e.g .vcf.gz) and b) to correctly preserve ordering in inputs.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1672 8bce386e-0d6e-43e0-b1ca-608082c0432d
Validate that either both or neither custom adapter sequence is provided.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1673 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added utility code to pull out the sequence dictionary from a tabix index file.

Useful for quickly validating consistency of the sequence dictionary (indirectly requested by Tim).
The GATK repo is nuts right now (we just moved to Maven) so although I think this code is working,
I may need to modify in a subsequent commit.  We shall see.



git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1674 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fixed a race condition causing occasional errors in AD and PL fields in multithreaded mode
Removed the side-effect of decoding genotypes when calling VariantContext.toString()


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1675 8bce386e-0d6e-43e0-b1ca-608082c0432d
IntelliJ keeps wanting to make this change.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1676 8bce386e-0d6e-43e0-b1ca-608082c0432d
Identify extensions .gz, .bgz, .bgzf as block-compressed vcf when writing VCF.
Add methods to create vcf, bcf, and block-compressed vcf explicitly as an alternative to determining format by examining file extension.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1677 8bce386e-0d6e-43e0-b1ca-608082c0432d