Mercurial > repos > ulfschaefer > vcfs2fasta
view vcfs2fasta.sh @ 14:f72039c5faa4 draft
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author | ulfschaefer |
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date | Wed, 16 Dec 2015 07:29:05 -0500 |
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#!/bin/bash echo $@ OUTPUT=$1 shift WITHMIXTURES=$1 shift COLUMNNS=$1 shift SAMPLENS=$1 shift REFERENCE=$1 shift INCLUDE=$1 shift EXCLUDE=$1 shift INPUT=$@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" export PATH=$PATH:$DIR CMD="vcfs2fasta.py --out $OUTPUT --input $INPUT" if [ $WITHMIXTURES != "NOTTHERE" ]; then CMD="$CMD --with-mixtures $WITHMIXTURES" fi if [ $COLUMNNS != "NOTTHERE" ]; then CMD="$CMD --column-Ns $COLUMNNS" fi if [ $SAMPLENS != "NOTTHERE" ]; then CMD="$CMD --sample-Ns $SAMPLENS" fi if [ $REFERENCE != "NOTTHERE" ]; then CMD="$CMD --reference $REFERENCE" fi if [ $INCLUDE != "NOTTHERE" ]; then CMD="$CMD --include INCLUDE" fi if [ $EXCLUDE != "NOTTHERE" ]; then CMD="$CMD --exclude EXCLUDE" fi echo $CMD eval $CMD