better support for manta

brentp · Dec 11, 2020 · 1a660d4 · 1a660d4
1 parent 8c2fec0
commit 1a660d4
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/duphold.nimble b/duphold.nimble
@@ -18,7 +18,7 @@ license       = "MIT"
 
 # Dependencies
 
-requires "hts >= 0.3.0", "genoiser >= 0.2.2",  "docopt >= 0.6.8"
+requires "hts >= 0.3.8", "genoiser >= 0.2.7",  "docopt >= 0.6.8"
 srcDir = "src"
 installExt = @["nim"]
 

diff --git a/src/duphold.nim b/src/duphold.nim
@@ -519,7 +519,9 @@ proc annotate*(snps:snpset, variant:Variant, sample_i:int) =
   if len(snps.starts) == 0: return
 
   # dont annotate BNDs (or INVs)
-  if ':' in variant.ALT[0] or variant.ALT[0] == "<INV>": return
+  var alt = variant.ALT[0]
+  if (':' in alt and ('[' in alt or ']' in alt)) or alt == "<INV>": return
+
   var dhgt = newSeq[int32](5 * variant.vcf.n_samples)
   get_or_empty(variant, "DHGT", dhgt, 5)
   dhgt[5*sample_i] = 0

diff --git a/src/dupholdpkg/version.nim b/src/dupholdpkg/version.nim
@@ -1 +1 @@
-const dupholdVersion* = "0.2.1"
+const dupholdVersion* = "0.2.2"