- removing unnecessary storage of a string in the Read Ends in Mark
Duplicates
- clarifying the size of ReadEndsForMarkDuplicates
Merge pull request #89 from broadinstitute/nh_remove_uncessessary_mark_duplicates_storing_read_name

- removing unnecessary storage of a string in the Read Ends in Mark
Updating the minimum number of times that the BAIT_INTERVALS (in CalculateHsMetrics) and TARGET_INTERVALS (in CollectTargetedMetrics) must be set to one.
Merge pull request #91 from broadinstitute/nh_update_calc_hs_metrics_for_min_interval_lists

Updating the minimum number of times that the BAIT_INTERVALS (in Calcula...
Release 1.122

Release 1.122
Improvement to handle 'mismatching' ref alleles for indel comparison conditions.
If ref allele in truth does not match ref allele in call, then verify first that the shorter ref allele string is the prefix of the longer, and then
append the remainder of the longer ref allele (i.e. that which follows the prefix) onto the shorter's ref and genotype alleles.
Changed extension for summary and detail metrics file.  Replacing old test data metrics files with ones with new extensions
Results of review - consolidated if statements, commented further
Merge pull request #90 from broadinstitute/gg_handle_ref_allele_mismatch_right

Improvement to handle 'mismatching' ref alleles for indel comparison conditions.  Also changed default extension of metrics files produced by the tool
updating the genotype concordance scheme to have called variants that
are filtered be counted as though they are missing
Merge pull request #92 from broadinstitute/nh_update_genotype_concordance_scheme

updating the genotype concordance scheme to have called variants that
Picard release 1.123

Picard release 1.123
This makes a fundamental change to how we run Picard.  We now have a
single JAR (command line program), rather than multiple JAR (one per
tool). In this brave new world, the single command line program is given
the the command line program name (ex. SamView) to specify which tool to
run.  We also provide a convenient summary of all of the tools
available.

For the developers, we add a facility to add new command line programs
to the single JAR, by extending the PicardCommandLine and adding the
package name(s) for us to search for classes that extend
CommandLineProgram.  The usage is now put in
CommandLineProgramProperties, where we can also specify short usages
(for the summary help message), program versions, and program groups.
The latter is useful for grouping tools that operate on common filetypes
or have similar function (ex. SAM/BAM).

We made a number of new tools public, coming from our internal toolset.
These include: BaitDesigner, CalculateReadGroupChecksum, CheckTerminatorBlock,
CollectIlluminaBasecallingMetrics, CollectIlluminaLaneMetrics,
CollectJumpingLibraryMetrics, CollectOxoGMetrics,
CollectQualityYieldMetrics, CollectRrbsMetrics, GatherVcfs,
LiftOverIntervalList, ScatterIntervalsByNs, and SplitSamByLibrary.
These may prove useful, or not.

Enjoy!
Merge pull request #93 from broadinstitute/nh_single_clp_v2

This makes a fundamental change to how we run Picard.  We now have a
New program FilterVcf that provides simple hard filtering functionality for VCFs.
Merge pull request #95 from broadinstitute/tf_hard_filtering

New program FilterVcf that provides simple hard filtering functionality ...
Added SAM/BAM/CRAM converter tests. This relies on the jc_cram_changes branch of the htsjdk.
Output CRAM from MarkDuplicates.
Rebase fixes.
SamReader conversion of Picard public.
Deprecation changes.
Added common argument for reference fasta to support CRAM input/output.
Reference fasta should be optional.
Use SamReaderFactory makeDefault with reference sequence whenever possible to allow for CRAM support.

Rebase changes.