Argument parsing, usage statement, and small improvements for countKmers #11
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standage
commented
Feb 15, 2019
| @@ -1,72 +0,0 @@ | |||
| HAWK version 0.9.8 | |||
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This file is redundant with README.md, and some parts are out of date. Better to just drop it.
| CATCMD="bunzip2 -c" | ||
| else | ||
| CATCMD=cat | ||
| fi |
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Here is where the compression is autodetected.
standage
commented
Feb 15, 2019
| jellyfishDir=/home/atif/jellyfish-Hawk/bin #directory where jellyfish is installed | ||
| sortDir=/home/atif/coreutils/deps/bin #directory where parallel sort is installed | ||
| #!/usr/bin/env bash | ||
| set -eo pipefail |
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It's helpful to halt execution if something goes wrong. Makes it easier to isolate the point of failure if it doesn't just try to keep going to the next sample.
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Rolled back the text about Jellyfish 2. |
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Thank you so much for your modifications! Incorporated a few. We are working on a few things. We will take care of the rest once that's done. |
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I made a few changes to the
countKmersscript for my own use, and thought they might be useful for others as well../countKmers -h.gzor not and dynamically determines whether to usezcatorcat, again so users don't have to modify the scriptI also updated
README.mdto reflect these changes,and the fact that Jellyfish 2 is a suitable alternative to the modified version of Jellyfish bundled with HAWK which seems to be giving some users issues.