Add cram support for RetroSeq#25

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maarten-k wants to merge 10 commits intotk2:masterfrom

Commits on Jan 28, 2021

Commits on Jul 20, 2022

[feature] cram works as input: instead of looking only for the presents of bam indexes also crai indexes are checked for presents
maarten-k
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[fix] samtools tried to extract negative starting regions in small decoys contigs. Now the start is at least 0
maarten-k
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[fix] small typo and copy and paste error
maarten-k
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Commits on Jul 31, 2022

When using cram files, only decode the field that is necessary. Benchmark 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 …
maarten-k
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Commits on Aug 5, 2022

Set a minimum version of samtools
maarten-k
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Commits on Oct 19, 2022