https://github.com/splatlab/squeakr
Revision dee045965e86ff9f0df2012d28f5631f0993cb35 authored by Shaun Jackman on 27 February 2018, 16:56:18 UTC, committed by Shaun Jackman on 27 February 2018, 16:59:24 UTC
1 parent 6507097
Tip revision: dee045965e86ff9f0df2012d28f5631f0993cb35 authored by Shaun Jackman on 27 February 2018, 16:56:18 UTC
qf_serialize: Add filename to error message
qf_serialize: Add filename to error message
Tip revision: dee0459
lognumslots.sh
#!/bin/bash
# This script takes as input the path to the output file of 'ntCard'. It then
# calculates log of the number of slots needed by Squeakr to count k-mers.
F0=`grep -P "^F0\t" $1 | cut -f2- -d$'\t'`
f1=`grep -P "^f1\t" $1 | cut -f2- -d$'\t'`
f2=`grep -P "^f2\t" $1 | cut -f2- -d$'\t'`
fgt2=$[ $F0 - $f1 - $f2 ]
ns=$[ $f1 + 2 * $f2 + 3 * $fgt2 ]
echo "x=$ns;l2=l(x)/l(2);s=scale;scale=0;l2ru=l2+1-(l2%1);np2=2^(l2ru/1);scale=s;if(x > (0.9*np2)) { l2ru=l2ru+1; np2=2*np2; }; s=scale; scale=0; print l2ru/1; scale=s;" | bc -l
echo
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