Accept PDH on command line.

[lightning.git] / pca.go

diff --git a/pca.go b/pca.go
index 41e3a7877f2847bfaed98bf3f583a9cd0842841a..121925d4c59d9833d37aabb397fa3a1bb0cc2243 100644 (file)
--- a/pca.go
+++ b/pca.go
@@ -1,4 +1,8 @@
-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
 
 import (
        "bufio"
@@ -147,7 +151,7 @@ func (cmd *goPCA) RunCommand(prog string, args []string, stdin io.Reader, stdout
                retainNoCalls:  true,
                compactGenomes: map[string][]tileVariantID{},
        }
-       err = tilelib.LoadGob(context.Background(), input, strings.HasSuffix(*inputFilename, ".gz"), nil)
+       err = tilelib.LoadGob(context.Background(), input, strings.HasSuffix(*inputFilename, ".gz"))
        if err != nil {
                return 1
        }
@@ -162,7 +166,7 @@ func (cmd *goPCA) RunCommand(prog string, args []string, stdin io.Reader, stdout
        tilelib.Tidy()
 
        log.Print("converting cgs to array")
-       data, rows, cols, _ := cgs2array(tilelib)
+       data, rows, cols := cgs2array(tilelib, cgnames(tilelib), lowqual(tilelib), nil, 0, len(tilelib.variant))
        if *onehot {
                log.Printf("recode one-hot: %d rows, %d cols", rows, cols)
                data, _, cols = recodeOnehot(data, cols)