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