fix: adaptd contig_priors to used contig name style (#489)

snappy_wrappers/wrappers/gcnv/contig_ploidy/wrapper.py

@@ -43,14 +43,24 @@
 export OMP_NUM_THREADS={snakemake.threads}
 export THEANO_FLAGS="base_compiledir=$TMPDIR/theano_compile_dir"
 
+# Get contig name style
+grep "SN:chr" {snakemake.input.interval_list} && true
+exit_status=$?
+if [[ exit_status == 0]] ; then
+    STYLE="chr"
+else
+    STYLE=""
+fi
+
+
 PRIORS=$TMPDIR/ploidy_priors.tsv
 echo -e "CONTIG_NAME\tPLOIDY_PRIOR_0\tPLOIDY_PRIOR_1\tPLOIDY_PRIOR_2\tPLOIDY_PRIOR_3" \
 > $PRIORS
 for i in {{1..22}}; do
-    echo -e "$i\t0\t0.01\t0.98\t0.01" >> $PRIORS
+    echo -e "$STYLE$i\t0\t0.01\t0.98\t0.01" >> $PRIORS
 done
-echo -e "X\t0.01\t0.49\t0.49\t0.01" >> $PRIORS
-echo -e "Y\t0.495\t0.495\t0.01\t0" >> $PRIORS
+echo -e "${STYLE}X\t0.01\t0.49\t0.49\t0.01" >> $PRIORS
+echo -e "${STYLE}Y\t0.495\t0.495\t0.01\t0" >> $PRIORS
 
 set -x