add support for picard-style .bam/.bai indexes #103
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Picard and GATK generate .bam/.bai rather than .bam/.bam.bai index names. This commit adds functionality which checks if .bam.bai exists, and if not falls back .bai (or .bam.bti).
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Picard (and by its virtue, GATK), use .bam/.bai indexes.
This adds a check for file existence to the index open, so that we can check if we're working with standard .bam.bai or .bai indexes.