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ohlab / GRiD

Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x).
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Implement option -e that defines the reads file extension #7

Closed nigiord closed 5 years ago

nigiord commented 5 years ago

Following discussion in #6 , this pull request simply adds an option to define the extension of the file containing reads. Support any extension as well as zipped files, default to 'fastq' as before.

Example tests described here work fine with a gzipped version of the mock_reads.fastq file. Outputs are not affected.

This pull request could become obsolete if the handling of inputs is reworked to allow SAM/BAM files, but is temporary measure for large analysis where it is not desired to uncompressed archived fastq.gz files.

ohlab commented 5 years ago

@nigiord Thanks. I'll release a new version as soon as i sort out SAM/BAM inputs