comparison vcfs2fasta.sh @ 22:96f393ad7fc6 draft default tip

Uploaded
author ulfschaefer
date Wed, 23 Dec 2015 04:50:58 -0500
parents f72039c5faa4
children
comparison
equal deleted inserted replaced
21:b09ffe50c378 22:96f393ad7fc6
1 #!/bin/bash
2
3 echo $@
4
5 OUTPUT=$1
6 shift
7 WITHMIXTURES=$1
8 shift
9 COLUMNNS=$1
10 shift
11 SAMPLENS=$1
12 shift
13 REFERENCE=$1
14 shift
15 INCLUDE=$1
16 shift
17 EXCLUDE=$1
18 shift
19 INPUT=$@
20
21 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
22 export PATH=$PATH:$DIR
23
24 CMD="vcfs2fasta.py --out $OUTPUT --input $INPUT"
25
26 if [ $WITHMIXTURES != "NOTTHERE" ]; then
27 CMD="$CMD --with-mixtures $WITHMIXTURES"
28 fi
29
30 if [ $COLUMNNS != "NOTTHERE" ]; then
31 CMD="$CMD --column-Ns $COLUMNNS"
32 fi
33
34 if [ $SAMPLENS != "NOTTHERE" ]; then
35 CMD="$CMD --sample-Ns $SAMPLENS"
36 fi
37
38 if [ $REFERENCE != "NOTTHERE" ]; then
39 CMD="$CMD --reference $REFERENCE"
40 fi
41
42 if [ $INCLUDE != "NOTTHERE" ]; then
43 CMD="$CMD --include INCLUDE"
44 fi
45
46 if [ $EXCLUDE != "NOTTHERE" ]; then
47 CMD="$CMD --exclude EXCLUDE"
48 fi
49
50 echo $CMD
51 eval $CMD