make IVA compatible with new 'samtools sort' syntax

sanger-pathogens / iva

de novo virus assembler of Illumina paired reads

http://sanger-pathogens.github.io/iva/

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make IVA compatible with new 'samtools sort' syntax #61

Closed satta closed 8 years ago

satta commented 8 years ago

This PR adds support for the new samtools sort syntax introduced in version 1.2. For older versions, the legacy syntax is automatically used. Tested with samtools versions 1.3.1 and 0.1.20 from Homebrew (just checking if iva --test succeeds). Closes #57.