adding support for multi mappers
undid strand fix to bam paired file reader, doesn't work when input bam is unaligned
don't need to specify both --bam and --bampair for paired bams
fixing multiple mapping mate alignment
fixing merge conflict with multimapper
Merge pull request #6 from mgymrek/master

merging multimapper
Merge pull request #7 from mgymrek/multimapper

Merge pull request #6 from mgymrek/master
Merge pull request #8 from whitehead/master

merging multimapper changes and fix to paired bam alignment
Merge pull request #1 from mgymrek/master

merging multimapper changes and fix to paired bam alignment