fixed imports the point to the correct SamPairUtil so that intelliJ doesn't get confused when the GATK version is mismatched.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1906 8bce386e-0d6e-43e0-b1ca-608082c0432d
Writing the proper size to faked-out BCL files

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1907 8bce386e-0d6e-43e0-b1ca-608082c0432d
Adding the name of the file to the error string when the number of elements in the file doesn't match that reported in the header

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1909 8bce386e-0d6e-43e0-b1ca-608082c0432d
PO-326 Validating the PL attribute in SAMFileValidator

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1910 8bce386e-0d6e-43e0-b1ca-608082c0432d
PO-326 Validating the PL attribute in SAMFileValidator

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1911 8bce386e-0d6e-43e0-b1ca-608082c0432d
Make public.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1913 8bce386e-0d6e-43e0-b1ca-608082c0432d
PO-326 Updating test data to include the platform RG attribute

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1914 8bce386e-0d6e-43e0-b1ca-608082c0432d
Moved output directory creation to constructor. This way MarkDuplicatesTester subclass can create a metrics file in the correct directory

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1918 8bce386e-0d6e-43e0-b1ca-608082c0432d
Adding support for gzipped and block gzipped files in the BCL file faker

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1919 8bce386e-0d6e-43e0-b1ca-608082c0432d
Move BLOCK_COMPRESSED_EXTENSIONS to Tribble so all projects use the same set of extensions

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1920 8bce386e-0d6e-43e0-b1ca-608082c0432d
Various de-wildcarding of imports.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1921 8bce386e-0d6e-43e0-b1ca-608082c0432d
PO-326 Removing checking PL values

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1923 8bce386e-0d6e-43e0-b1ca-608082c0432d
Create Tabix indices for block-compressed VCFs
Unit test updates for INDEX_ON_THE_FLY and FORCE_BCF


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1924 8bce386e-0d6e-43e0-b1ca-608082c0432d
Deprecate VariantContextWriterFactory
Convert uses of VariantContextWriterFactory to VariantContextWriterBuilder
Minor unit test update


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1925 8bce386e-0d6e-43e0-b1ca-608082c0432d
Faker now produces the correct length faked files if the data in the run folder is compressed

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1927 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fixing unit tests for CheckIlluminaDirectories

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1928 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.112


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1929 8bce386e-0d6e-43e0-b1ca-608082c0432d
Addition of a simple SamRecordFilter that filters out secondary alignments but not supplementary records.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1931 8bce386e-0d6e-43e0-b1ca-608082c0432d
Changes to SamLocusIterator to a) check the mapping quality only once per sam record instead of at every base and b) add the ability to filter out non-PF reads during pileup construction.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1932 8bce386e-0d6e-43e0-b1ca-608082c0432d
First version of CollectWgsMetrics a program that calculates metrics for evaluating whole genome shotgun sequencing experiments.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1933 8bce386e-0d6e-43e0-b1ca-608082c0432d