Fix coordinates in hgvs annotations.

[lightning.git] / pca.go

diff --git a/pca.go b/pca.go
index 72580fdb78509a5c9a8e8d2c4c729b1c1b9d3a7d..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"
@@ -113,8 +117,8 @@ func (cmd *goPCA) RunCommand(prog string, args []string, stdin io.Reader, stdout
                        Name:        "lightning pca-go",
                        Client:      arvados.NewClientFromEnv(),
                        ProjectUUID: *projectUUID,
-                       RAM:         100000000000, // maybe 10x input size?
-                       VCPUs:       2,
+                       RAM:         300000000000, // maybe 10x input size?
+                       VCPUs:       16,
                        Priority:    *priority,
                }
                err = runner.TranslatePaths(inputFilename)
@@ -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
        }
@@ -162,11 +166,12 @@ 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)
        }
+       tilelib = nil
 
        log.Printf("creating matrix backed by array: %d rows, %d cols", rows, cols)
        mtx := array2matrix(rows, cols, data).T()