Mercurial > repos > ulfschaefer > phephenix
view vcfs2fasta.sh @ 19:9c63ab34838d draft default tip
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author | ulfschaefer |
---|---|
date | Thu, 14 Jul 2016 10:50:41 -0400 |
parents | f7494340ae7f |
children |
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#!/bin/bash echo $@ OUTPUT=$1 shift WITHMIXTURES=$1 shift COLUMNNS=$1 shift COLUMNGAPS=$1 shift SAMPLENS=$1 shift SAMPLEGAPS=$1 shift REFERENCE=$1 shift INCLUDE=$1 shift EXCLUDE=$1 shift STATS=$1 shift INPUT=$@ CMD="phenix.py vcf2fasta --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 [ $COLUMNGAPS != "NOTTHERE" ]; then CMD="$CMD --column-gaps $COLUMNGAPS" fi if [ $SAMPLENS != "NOTTHERE" ]; then CMD="$CMD --sample-Ns $SAMPLENS" fi if [ $SAMPLEGAPS != "NOTTHERE" ]; then CMD="$CMD --sample-gaps $SAMPLEGAPS" 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 if [ $STATS != "NOTTHERE" ]; then CMD="$CMD --with-stats $STATS" fi echo $CMD eval $CMD