| Previous changeset 6:74f595df6e51 (2016-06-16) Next changeset 8:f05fa489089b (2016-06-16) |
|
Commit message:
Uploaded |
|
modified:
vcfs2fasta.sh |
| b |
| diff -r 74f595df6e51 -r 29a682a7dd16 vcfs2fasta.sh --- a/vcfs2fasta.sh Thu Jun 16 06:39:51 2016 -0400 +++ b/vcfs2fasta.sh Thu Jun 16 06:40:02 2016 -0400 |
| [ |
| @@ -8,14 +8,20 @@ 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 $INPUT" @@ -28,20 +34,28 @@ CMD="$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" + CMD="$CMD --include $INCLUDE" fi if [ $EXCLUDE != "NOTTHERE" ]; then - CMD="$CMD --exclude EXCLUDE" + CMD="$CMD --exclude $EXCLUDE" fi echo $CMD |