Fix problem with genome backed by samtools/picard faidx files. In some cases, read bases would be returned shifted by one position.
Release Goby C/C++ APIs under the LGPL license version 3 to make it possible for companies to incorporate support for Goby formats in their tools. Thanks to Collin Hercus for the suggestion. Please note that part of the Goby Java APIs are already licensed under the LGPL (anything packaged under the Goby-io.jar file).

Conflicts:

	CHANGES.txt
Fix problem with genome backed by samtools/picard faidx files. In some cases, read bases would be returned shifted by one position.
Tags start at column 12, index 11. --preserve-all-tags could skip the first tag on some datasets (e.g., dataset where the first tag was not a MD:Z or RG:Z). Thanks to James Bonfield for reporting this problem.
 - Introduce interface for ReadsWriter. Introduce mock implementation to write reads to text. This is useful to write
   more intelligible JUnit tests.
 - fix a bug in reformat-compact-reads which did not trim quality scores for paired end reads correctly.
mode sam-to-compact now supports option --read-names-are-query-indices to indicate that the read names are integers
   (typically produced by compact-to-fasta from a chunk of a large file).

Conflicts:

	CHANGES.txt
C++ API: Support to set placed unmapped and clipleft/clipright with quality scores.
Tweak CHANGES.txt prior to 2.0.1 release.
updated version numbers for python and c++ APIs
Add pointer to latest stable branch.
compact-to-sam mode: fix bug where bam tags containing a colon character (:) would be truncated after the first
   colon. Thanks to Vadim Zalunin for reporting this problem.
remove idea project files
Add file3.fasta
Merge changes into stable.
Some speed optimizations.
Make plus coder the default for 2.1 release.
While STAR uses NH to store readMaxOccurence, GSNAP seems to put some other values in that field so we
             can't really trust these values in general. Disable for now on the stable branch.
Prepare CHANGES for 2.1 release.
A few tweaks to CHANGES and code.
Add support to push Goby jar(s) to maven local repository.