✅ add test reference dicts files

papaemmelab · Jan 23, 2024 · 3ef1e3a · 3ef1e3a
1 parent db0b4a0
commit 3ef1e3a
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Showing 8 changed files with 14 additions and 2 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -26,7 +26,7 @@ jobs:
             --tumor TEST \
             --tumorBam `pwd`/tests/data/tumor.bam \
             --refGenome `pwd`/tests/data/reference.fasta \
-            --outdir /app/results
+            --outdir `pwd`/results
       - name: Check result
         run: |
           if [ ! -f /app/results/TEST.purple.purity.tsv ]; then

diff --git a/tests/README b/tests/README
@@ -19,7 +19,7 @@ samtools view -b -o $TEST_NORMAL_BAM $ORIGINAL_NORMAL_BAM $REGION1 $REGION2
 samtools index $TEST_TUMOR_BAM
 samtools index $TEST_NORMAL_BAM
 
-# Build test Reference file
+# Build test Reference files
 ORIGINAL_REF=`isabl get-reference GRCh37`
 LOCAL_REF=gr37.fasta
 TEST_REF=reference.fasta
@@ -30,4 +30,6 @@ cp $ORIGINAL_REF.fai $LOCAL_REF.fai
 samtools faidx $LOCAL_REF $REGION1 >> $TEST_REF
 samtools faidx $LOCAL_REF $REGION2 >> $TEST_REF
 samtools faidx $TEST_REF
+samtools dict -a GRCh37 -s HUMAN $LOCAL_REF > $TEST_REF.dict
+bwa index $TEST_REF
 ```
diff --git a/tests/data/reference.fasta.amb b/tests/data/reference.fasta.amb
@@ -0,0 +1,2 @@
+200002 2 1
+77418 22583 N
diff --git a/tests/data/reference.fasta.ann b/tests/data/reference.fasta.ann
@@ -0,0 +1,5 @@
+200002 2 11
+0 1:100000-200000 (null)
+0 100001 1
+0 2:300000-400000 (null)
+100001 100001 0
diff --git a/tests/data/reference.fasta.bwt b/tests/data/reference.fasta.bwt
diff --git a/tests/data/reference.fasta.dict b/tests/data/reference.fasta.dict
@@ -0,0 +1,3 @@
+@HD	VN:1.0	SO:unsorted
+@SQ	SN:1:100000-200000	LN:100001	M5:a6cb0c5d3b0a027196d67fbd782a308a	UR:file:///work/isabl/home/arangooj/dev/purple/data/reference.fasta	AS:GRCh37	SP:HUMAN
+@SQ	SN:2:300000-400000	LN:100001	M5:7bdb46835543f5aedaea4e8a0f02689e	UR:file:///work/isabl/home/arangooj/dev/purple/data/reference.fasta	AS:GRCh37	SP:HUMAN
diff --git a/tests/data/reference.fasta.pac b/tests/data/reference.fasta.pac
diff --git a/tests/data/reference.fasta.sa b/tests/data/reference.fasta.sa