handle more chrMT namings

brentp · Apr 9, 2021 · 7be61a8 · 7be61a8
1 parent 87b8ffb
commit 7be61a8
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,7 @@
+v0.0.5
+======
++ handle more chrMT namings
+
 v0.0.4
 ============
 + plot aesthetics (#23)

diff --git a/src/seqcoverpkg/transcript.nim b/src/seqcoverpkg/transcript.nim
@@ -161,12 +161,17 @@ proc `%`*[T](table: TableRef[string, T]): JsonNode =
 
 proc get_chrom(chrom:string, dp:var Cover, fai:Fai): string =
   ## add or remove "chr" to match chromosome names.
+  const MTs = ["MT", "CHRM", "CHRMT", "M"]
   var chroms = dp.chromosomes(fai)
   if chrom in chroms: return chrom
   if chrom[0] != 'c' and ("chr" & chrom) in chroms:
     result = "chr" & chrom
   elif chrom[0] == 'c' and chrom.len > 3 and chrom[1] == 'h' and chrom[2] == 'r' and chrom[3..chrom.high] in chroms:
     result = chrom[3..chrom.high]
+  elif chrom.toUpperAscii in MTs: # try all the MT chroms.
+    for c in MTs:
+      if c in chroms:
+        return c
   else:
     raise newException(KeyError, "chromosome not found:" & chrom)