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added sam functionality, updated README, Write to SAM/BAM#1

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mjsull wants to merge 30 commits into
BeatsonLab-MicrobialGenomics:masterfrom
mjsull:master
Open

added sam functionality, updated README, Write to SAM/BAM#1
mjsull wants to merge 30 commits into
BeatsonLab-MicrobialGenomics:masterfrom
mjsull:master

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