change no variants in compound-het to warning

brentp · May 3, 2021 · eb32385 · eb32385
1 parent 0544428
commit eb32385
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/CHANGES.md b/CHANGES.md
@@ -7,6 +7,8 @@ v0.2.2
 + fix bug when creating huge zip files with make-gnotate (#86)
 + **NOTE**: change default min depth in slivar-functions.js to 6. (was 0)
 + don't hard-code tmp directory to /tmp (use $TMPDIR)
++ [compound-hets] dont fail if no usable variants were found, just issue warning.
+  this can happen for small chroms or regions when slivar was parallelized.
 
 v0.2.1
 ======

diff --git a/src/slivarpkg/comphet.nim b/src/slivarpkg/comphet.nim
@@ -305,7 +305,8 @@ proc main*(dropfirst:bool=false) =
   ivcf.close()
   stderr.write_line &"[slivar compound-hets] wrote {nwritten} variants that were part of a compound het."
   if ncsqs == 0:
-    quit &"[slvar compound-hets] no variants had any of the requested fields; unable to call compound hets"
+    stderr.write_line &"[slvar compound-hets] WARNING!!! no variants had any of the requested fields; unable to call compound hets!"
+    quit 0
 
   var summaryPath = getEnv("SLIVAR_SUMMARY_FILE")
   if summaryPath == "":