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…ts of bam indexes also crai indexes are checked for presents
…coys contigs. Now the start is at least 0
…mark with a small cram file a speedup of at least 2x in the discover phase. Bam files can still be used and do not benefit from this optimisation.
This is set to 1 version higher than actually needed since the CheckBinary function has issues to see that 1.15 Is higher than 1.9 (it does a string compare and not a numeric compare)
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This pull request enables RetroSeq to handle cram files. This is facilitated by using a modern version of samtools (newer than 1.10) and some changes in the code for checking files (e.g. also allow cram files when looking for cram.) Bam support is still supported.