Don't skip anomalous read pairs with samtools mpileup
Add TODOs
Fix path to SNP caller
Fix bugs leading to 0 coverage for inserts
Add missing column header to SNP files
Cleanup flanking coverage SNP filtering
Update Usage document
Gitignore final SNP lists
Merge branch 'feature/fix-coverage' into develop
Update version number in README
Merge branch 'release/0.1.3' into develop