X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/ba5dea916505730ed44af0655c820bd3d767be1e..e4839e500e2da73b476f095425c0347ae7c5de97:/tilelib_test.go

diff --git a/tilelib_test.go b/tilelib_test.go
index 0e7edd6759..5801b9baf3 100644
--- a/tilelib_test.go
+++ b/tilelib_test.go
@@ -1,7 +1,12 @@
-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
 
 import (
 	"bytes"
+	"regexp"
 	"strings"
 
 	"gopkg.in/check.v1"
@@ -32,69 +37,71 @@ gttattaataataacttatcatca
 }
 
 func (s *tilelibSuite) TestSkipOOO(c *check.C) {
+	matchAllChromosomes := regexp.MustCompile(".")
+
 	// tags appear in seq: 4, 0, 2 (but skipOOO is false)
 	tilelib := &tileLibrary{taglib: &s.taglib, skipOOO: false}
-	tseq, err := tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+	tseq, _, err := tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
 		s.tag[4]+
 		"ggggggggggggggggggggggg\n"+
 		s.tag[0]+
 		"cccccccccccccccccccc\n"+
 		s.tag[2]+
-		"\n"))
+		"\n"), matchAllChromosomes, false)
 	c.Assert(err, check.IsNil)
 	c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{4, 1}, {0, 1}, {2, 1}}})
 
 	// tags appear in seq: 0, 1, 2 -> don't skip
 	tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
-	tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+	tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
 		s.tag[0]+
 		"cccccccccccccccccccc\n"+
 		s.tag[1]+
 		"ggggggggggggggggggggggg\n"+
 		s.tag[2]+
-		"\n"))
+		"\n"), matchAllChromosomes, false)
 	c.Assert(err, check.IsNil)
 	c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {2, 1}}})
 
 	// tags appear in seq: 2, 3, 4 -> don't skip
 	tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
-	tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+	tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
 		s.tag[2]+
 		"cccccccccccccccccccc\n"+
 		s.tag[3]+
 		"ggggggggggggggggggggggg\n"+
 		s.tag[4]+
-		"\n"))
+		"\n"), matchAllChromosomes, false)
 	c.Assert(err, check.IsNil)
 	c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{2, 1}, {3, 1}, {4, 1}}})
 
 	// tags appear in seq: 4, 0, 2 -> skip 4
 	tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
-	tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+	tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
 		s.tag[4]+
 		"cccccccccccccccccccc\n"+
 		s.tag[0]+
 		"ggggggggggggggggggggggg\n"+
 		s.tag[2]+
-		"\n"))
+		"\n"), matchAllChromosomes, false)
 	c.Assert(err, check.IsNil)
 	c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {2, 1}}})
 
 	// tags appear in seq: 0, 2, 1 -> skip 2
 	tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
-	tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+	tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
 		s.tag[0]+
 		"cccccccccccccccccccc\n"+
 		s.tag[2]+
 		"ggggggggggggggggggggggg\n"+
 		s.tag[1]+
-		"\n"))
+		"\n"), matchAllChromosomes, false)
 	c.Assert(err, check.IsNil)
 	c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}}})
 
 	// tags appear in seq: 0, 1, 1, 2 -> skip second tag1
 	tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
-	tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+	tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
 		s.tag[0]+
 		"cccccccccccccccccccc\n"+
 		s.tag[1]+
@@ -102,13 +109,13 @@ func (s *tilelibSuite) TestSkipOOO(c *check.C) {
 		s.tag[1]+
 		"ggggggggggggggggggggggg\n"+
 		s.tag[2]+
-		"\n"))
+		"\n"), matchAllChromosomes, false)
 	c.Assert(err, check.IsNil)
 	c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {2, 1}}})
 
 	// tags appear in seq: 0, 1, 3, 0, 4 -> skip second tag0
 	tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
-	tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+	tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
 		s.tag[0]+
 		"cccccccccccccccccccc\n"+
 		s.tag[1]+
@@ -118,19 +125,19 @@ func (s *tilelibSuite) TestSkipOOO(c *check.C) {
 		s.tag[0]+
 		"ggggggggggggggggggggggg\n"+
 		s.tag[4]+
-		"\n"))
+		"\n"), matchAllChromosomes, false)
 	c.Assert(err, check.IsNil)
 	c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {3, 1}, {4, 1}}})
 
 	// tags appear in seq: 0, 1, 3 -> don't skip
 	tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
-	tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+	tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
 		s.tag[0]+
 		"cccccccccccccccccccc\n"+
 		s.tag[1]+
 		"ggggggggggggggggggggggg\n"+
 		s.tag[3]+
-		"\n"))
+		"\n"), matchAllChromosomes, false)
 	c.Assert(err, check.IsNil)
 	c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {3, 1}}})
 }