Added help etc
Merge pull request #1 from jmchilton/master

Add citations.
added bwa aln, samse, and sample combined wrapper. fixed help typos in bwa-mem
Test data for bwa-mem
Small tweaks to bwa-mem suggested by bjorn
Create README.md
first vresion of complete bwa and bwa-mem tools
fixed bwa_index.loc.sample
added tool_data_tables_conf.xml.sample and bwa_mem_index.loc.sample. fixed typo in tool_dependencies.xml
Delete bwa_index.loc.sample
Fixed samtools postprocessing to produce sorted ban files and updated test data
fix small typo