indel tests

test/test_indel_del_ont.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+if [ $# -ne 1 ]
+then
+    echo "usage: $0 <path to picard.jar>"
+    exit 65
+fi
+
+REF=../test_data/Homo_sapiens_chr22_assembly19.fasta
+
+command -v addsnv.py >/dev/null 2>&1 || { echo "addsnv.py isn't installed" >&2; exit 65; }
+
+if [ ! -e $1 ]
+then
+    echo "cannot find picard.jar"
+    exit 65
+fi
+
+
+addindel.py -v ../test_data/test_ont_indel_del.txt -f ../test_data/testregion_ont.bam -r $REF -o ../test_data/testregion_ont_mut.bam -n 5 --picardjar $1 --aligner minimap2 --alignopts x:map-ont --seed 1234 --ignorepileup --single --mindepth 4
+
+samtools sort ../test_data/testregion_ont_mut.bam > ../test_data/testregion_ont_mut.sorted.bam
+mv ../test_data/testregion_ont_mut.sorted.bam ../test_data/testregion_ont_mut.bam
+samtools index ../test_data/testregion_ont_mut.bam
+
+#if [ $? -ne 0 ]
+#then
+# echo "addsnv.py failed. Are all the prequisites installed?"
+# exit 1 
+#else
+#  samtools mpileup -ugf $REF ../test_data/testregion_mut.bam | bcftools call -vm
+#fi

test/test_indel_ins_ont.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+if [ $# -ne 1 ]
+then
+    echo "usage: $0 <path to picard.jar>"
+    exit 65
+fi
+
+REF=../test_data/Homo_sapiens_chr22_assembly19.fasta
+
+command -v addsnv.py >/dev/null 2>&1 || { echo "addsnv.py isn't installed" >&2; exit 65; }
+
+if [ ! -e $1 ]
+then
+    echo "cannot find picard.jar"
+    exit 65
+fi
+
+
+addindel.py -v ../test_data/test_ont_indel_ins.txt -f ../test_data/testregion_ont.bam -r $REF -o ../test_data/testregion_ont_mut.bam -n 5 --picardjar $1 --aligner minimap2 --alignopts x:map-ont --seed 1234 --ignorepileup --single --mindepth 4
+
+samtools sort ../test_data/testregion_ont_mut.bam > ../test_data/testregion_ont_mut.sorted.bam
+mv ../test_data/testregion_ont_mut.sorted.bam ../test_data/testregion_ont_mut.bam
+samtools index ../test_data/testregion_ont_mut.bam
+
+#if [ $? -ne 0 ]
+#then
+# echo "addsnv.py failed. Are all the prequisites installed?"
+# exit 1 
+#else
+#  samtools mpileup -ugf $REF ../test_data/testregion_mut.bam | bcftools call -vm
+#fi

test_data/test_ont_indel_del.txt

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+22 34169764 34169864 1.0 DEL

test_data/test_ont_indel_ins.txt

@@ -0,0 +1 @@
+22 34169864 34169864 1.0 INS GG