allow detection of long indels

Long deletions were filtered out by legacy code which considered gaps as
mismatches.
indicate that 0.9.9 is new stable revision
set the haplotype calling window with --haplotype-length

This is a synonym for --max-complex-gap, but I wanted to ensure that
users were clear on the meaning of this parameter.

If you want to call haplotypes, then increase --haplotype-length.  (It's
3bp by default.)
avoid errors with soft clipped sequence at the beginning of reference

This leads to errors typically in chrM, as the circular nature of this
chromosome means many reads are mapped with soft clips at position 0.
set correct merge order using new bamtools method
resolve read group header parsing bug, empty alignment bug

When read groups had colons in them, they were not parsed properly.

When reads were aligned as wholly soft-clipped, the allele parsing segfaulted.
addition of contamination estimates into GLs

This is a first pass solution, and should probably not be used in production.
This commit is for future reference.
per-read group contamination estimates

This is a checkpoint.  This functionality is relatively stable.
partial haplotype observations

Use all read evidence, even when calling haplotypes, by utilizing equivalencies
between partial observations of a haplotype and the putative alleles at the
site.

Observations which partially support a number of haplotypes have their
probability mass divided amongst the alleles they support when calculating
genotype likelihoods.

This provision resolves sensitivity issues caused by
increased spanning coverage required to call small variants when using larger
--haplotype-length values.

The adjustment to genotype likelihood calculations currently requires the use
of the new GL calculation routine provided when enabling --prob-contamination
0, or providing a per-sample contamination estimate file via
--contamination-estimates.
Setting Release-Version v9.9.1
balanced observations for indels (indels)

For insertions (currently), require that the reference observations at the
haplotype containing the insertion flank the insertion by a combined number of
bases that is the same as the length of the insertion.

This normalizes the likelihood calculations for insertions.

Normalization is (currently) provided implicitly for deletions in that
reference bias prevents the mapping of longer deletions.  This effect is
stronger than the sum of bases effect driving bias problems for insertions.
add version_git.h
properly include Contamination.*
include autoversion in default build path

Now, the version will include the git commit id from the repo!
versioning fix (add version_git.h to dependencies)
updated .gitignore, added CNV BED example
parameter changes, --bam-list and --region

Allow a bam file list to be provided on the command line.

Allow the use of '-' as a region separator in region strings.
remove spurious N alleles from output

Now that haplotype construction occurs at every base, the removal of part-null
alleles needs to occur also in the genotypeAlleles routine (which establishes
which alleles should be used for genotyping).
updated bamtools
remove partial component from RO in VCF output