From: Tom Clegg <tom@curii.com>
Date: Tue, 10 Jan 2023 15:00:16 +0000 (-0500)
Subject: Fix -min-coverage calculation broken when -case-control-only=true.
X-Git-Url: https://git.arvados.org/lightning.git/commitdiff_plain/d9ece5bc1d94a9b0536516d67249beb9ac927d2a

Fix -min-coverage calculation broken when -case-control-only=true.

refs #19868

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
---

diff --git a/slicenumpy.go b/slicenumpy.go
index 0e956a43d5..a22d662b74 100644
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -316,6 +316,13 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
 		cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
 	}
 
+	// cgnamemap[name]==true for samples that we are including in
+	// output
+	cgnamemap := map[string]bool{}
+	for _, name := range cmd.cgnames {
+		cgnamemap[name] = true
+	}
+
 	{
 		samplesOutFilename := *outputDir + "/samples.csv"
 		log.Infof("writing sample metadata to %s", samplesOutFilename)
@@ -532,7 +539,7 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
 					if cmd.filter.MaxTag >= 0 && cg.StartTag > tagID(cmd.filter.MaxTag) {
 						return errSkip
 					}
-					if !matchGenome.MatchString(cg.Name) {
+					if !cgnamemap[cg.Name] {
 						continue
 					}
 					// pad to full slice size