v0.5

Added features, some improvements in alignment (accuracy), and minor bugfixes.

1. Added parameter -N [INT] to output secondary alignments
2. Base level alignment parameters can now be specified from command line -A -B -E -O
3. Improved MAPQ calculation: calculating them from alignments (if alignment mode) instead of from seeds.
4. Update default base-level alignment parameters for better alignments around indels.
5. Added Quality values, AS:i and NM:i tags to SAM output.

See INDEL/SNV calling benchmark in README.