Add filter options to export cmd.

[lightning.git] / filter.go

diff --git a/filter.go b/filter.go
index c66ea0ad0f77b3542128a88fa98bdf6e22d94df8..9d43abea608d98d9be8aec53934f2383c86fb0b1 100644 (file)
--- a/filter.go
+++ b/filter.go
@@ -65,9 +65,12 @@ func (f *filter) Apply(tilelib *tileLibrary) {
        // f.MinCoverage.
        mincov := int(2*f.MinCoverage*float64(len(tilelib.compactGenomes)) + 1)
 TAG:
-       for tag := 0; tag < len(tilelib.variant) && tag < f.MaxTag; tag++ {
+       for tag := 0; tag < len(tilelib.variant) && (tag < f.MaxTag || f.MaxTag < 0); tag++ {
                tagcov := 0
                for _, cg := range tilelib.compactGenomes {
+                       if len(cg) < tag*2+2 {
+                               continue
+                       }
                        if cg[tag*2] > 0 {
                                tagcov++
                        }
@@ -79,8 +82,10 @@ TAG:
                        }
                }
                for _, cg := range tilelib.compactGenomes {
-                       cg[tag*2] = 0
-                       cg[tag*2+1] = 0
+                       if len(cg) > tag*2 {
+                               cg[tag*2] = 0
+                               cg[tag*2+1] = 0
+                       }
                }
        }