Conflicts:
	public/biopet-framework/pom.xml

Tsv mod

This fixes/closes #73

Changes:
* Use VCF naming conventions for default fields
* Spelling/typos
* Adding the option to change the separator
* Adding option to change amount of decimals for numeric values
* Fixes sorting function
* adding tests

See merge request !153

Quality scores based on formatter
max nr of decimals can be set by flag
separators can be changed by flag

Fixed parsing of empty values

See merge request !152

Fix vcfwriters

This branch fixes issues #152 and #153, and it includes test cases for #152.

See merge request !151

added extra options to bowtie

See merge request !150

adding checkAllelesVcfInBamTest stub and adding bgzipped and tabixed VCF files for tools that need indexed files

Patch meta in summary

This pull request adds a `meta` entry to the root of each summary JSON file. The contents of the meta is:

`last_commit_hash`: the commit hash of the repository when the JAR was built. If the repository has uncommitted changes, `-dirty` is appended to the commit hash.

`pipeline_version`: the version of the pipeline (the one we put in the `pom.xml` file).

This information is static across all modules and subpipelines to any given pipeline run, so I decided to put this in the root.

See merge request !144

Patch extractalignedfastq

The changeset + commit message should be clear enough :). This was caused by a passing a wrong variable to the `BasicFastqWriter` constructor.

See merge request !142

Fix intervals

Fix for #128

See merge request !145