Removed test_data directory

Author: viklund

bin/uppmax_make_test_data.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+module load bioinfo-tools
+module load samtools
+
+set -x
+
+CHR="1 2"
+FN="1-2"
+
+BASEDIR=/proj/a2009002/webexport/opendata/HiSeqX_CEPH/CEP-1-7/03-BAM
+BASEFILE=CEP-1-7.clean.dedup.recal
+
+OUT="$BASEFILE.chr$FN"
+
+if [ ! -f $OUT.bam ]; then
+    samtools view -bh "$BASEDIR/$BASEFILE.bam" $CHR > $OUT.bam
+fi
+
+if [ ! -f $OUT.bam.bai ]; then
+    samtools index $OUT.bam
+fi
+
+if [ ! -f $OUT.fq.gz ]; then
+    samtools bam2fq $OUT.bam | gzip - > $OUT.fq.gz
+fi