Mercurial > repos > ulfschaefer > phephenix
diff vcfs2fasta.sh @ 0:cb29f95c7b88 draft
Uploaded
author | ulfschaefer |
---|---|
date | Mon, 09 May 2016 09:27:06 -0400 |
parents | |
children | 29a682a7dd16 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfs2fasta.sh Mon May 09 09:27:06 2016 -0400 @@ -0,0 +1,48 @@ +#!/bin/bash + +echo $@ + +OUTPUT=$1 +shift +WITHMIXTURES=$1 +shift +COLUMNNS=$1 +shift +SAMPLENS=$1 +shift +REFERENCE=$1 +shift +INCLUDE=$1 +shift +EXCLUDE=$1 +shift +INPUT=$@ + +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 [ $SAMPLENS != "NOTTHERE" ]; then + CMD="$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