Mercurial > repos > ulfschaefer > vcfs2fasta
changeset 2:bff397ce7794 draft
Deleted selected files
| author | ulfschaefer |
|---|---|
| date | Wed, 16 Dec 2015 07:23:27 -0500 |
| parents | 01bd7d27089d |
| children | 13ff9dbcd580 |
| files | vcfs2fasta/vcfs2fasta.sh |
| diffstat | 1 files changed, 0 insertions(+), 51 deletions(-) [+] |
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--- a/vcfs2fasta/vcfs2fasta.sh Wed Dec 16 07:23:12 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ -#!/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