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README.md

@@ -25,5 +25,5 @@ sudo apt install cmake libclang-dev
 * Somatic Variants of chrM (25) 
 ```
 zcat /data/longreads_basic_pipe/*/diag/somatic_variants.json.gz | \
-jq -L ./jq_filters -C 'include "jq_filters"; [.data[] | select(.position.contig == 25 and n_in_constit <= 1) | format]'
+jq -L ./jq_filters -C 'include "jq_filters"; [.data[] | select(contig("chrM") and n_in_constit <= 1) | format]'
 ```

jq_filters/jq_filters.jq

@@ -4,3 +4,13 @@ def format:
 
 def n_alt_in_constit:
 	(.annotations | map(select(.ConstitAlt != null).ConstitAlt) // [0] | .[0]);
+
+def contig_to_num(contig):
+  if contig == "chrX" then 23
+  elif contig == "chrY" then 24
+  elif contig == "chrM" then 25
+  else (contig | ltrimstr("chr") | tonumber // 255) end;
+
+def contig(contig_str):
+	.position.contig == contig_to_num(contig_str);
+