Start of codon correction update#21
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susannah-b wants to merge 462 commits intoChrisHIV:masterfrom
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…dentical region of the same reference. (Contig pieces now have a piece number in their name.)
…les with same names exist in the working directory (formerly we silently overwrote them). We now don't bother copying the reads to the working dir if they're already there. We now quit if unzipping doesn't remove the .gz from the read file names instead of assuming it does.
…this (if needed) to config.sh, to avoid this taking precedence over the more robust trimmomatic binary in conda shiver
…ere triggering exit as intended
…nction for testing file existence
…rence file didn't work
…ence but no coordinates
…l merging of CodonCorrectionInit.sh with shiver_init.sh, when a single alignment may be used with some references not wanted for codon correction, like HXB2)
…sitions being less than their start positions
…ides) to be a multiple of 3
… to log files for a quieter stdout
…ed in the coords file
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Update to shiver to include CodonCorrection.sh and surrounding scripts, which correct genes from within the shiver remap consensus files, although are not yet integrated into a final full genome product. Includes basic shiver implementation which currently has an error with the init directory (can be removed or fixed as it only involves a few lines of code).
Several hundred commits 'ahead' due to rebase issues - I haven't been able to resolve this but if there's anything I can adjust let me know - otherwise I'm hoping they can be resolved as the same commits exist in the upstream repo.
Please see the CodonCorrectionDoc PDF for further information on usage and current project status.