X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/3bd8fa5ccd85a4f8155ab2837433671aff5ddf38..e4839e500e2da73b476f095425c0347ae7c5de97:/tilelib_test.go

diff --git a/tilelib_test.go b/tilelib_test.go
index 4e6ca0afa5..5801b9baf3 100644
--- a/tilelib_test.go
+++ b/tilelib_test.go
@@ -1,125 +1,143 @@
-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"
 )
 
-type tilelibSuite struct{}
+type tilelibSuite struct {
+	tag    []string
+	taglib tagLibrary
+}
 
 var _ = check.Suite(&tilelibSuite{})
 
-func (s *tilelibSuite) TestSkipOOO(c *check.C) {
-	var taglib tagLibrary
-	err := taglib.Load(bytes.NewBufferString(`>0000.00
+func (s *tilelibSuite) SetUpSuite(c *check.C) {
+	fasta := `>0000.00
 ggagaactgtgctccgccttcaga
 acacatgctagcgcgtcggggtgg
 gactctagcagagtggccagccac
 cctcccgagccgagccacccgtca
 gttattaataataacttatcatca
-`))
+`
+	err := s.taglib.Load(bytes.NewBufferString(fasta))
 	c.Assert(err, check.IsNil)
+	for _, seq := range strings.Split(fasta, "\n") {
+		if len(seq) > 0 && seq[0] != '>' {
+			s.tag = append(s.tag, seq+"\n")
+		}
+	}
+}
+
+func (s *tilelibSuite) TestSkipOOO(c *check.C) {
+	matchAllChromosomes := regexp.MustCompile(".")
 
 	// tags appear in seq: 4, 0, 2 (but skipOOO is false)
-	tilelib := &tileLibrary{taglib: &taglib, skipOOO: false}
-	tseq, err := tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-gttattaataataacttatcatca
-ggggggggggggggggggggggg
-ggagaactgtgctccgccttcaga
-cccccccccccccccccccc
-gactctagcagagtggccagccac
-`))
+	tilelib := &tileLibrary{taglib: &s.taglib, skipOOO: false}
+	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"), 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: &taglib, skipOOO: true}
-	tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-ggagaactgtgctccgccttcaga
-cccccccccccccccccccc
-acacatgctagcgcgtcggggtgg
-ggggggggggggggggggggggg
-gactctagcagagtggccagccac
-`))
+	tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
+	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"), 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: &taglib, skipOOO: true}
-	tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-gactctagcagagtggccagccac
-cccccccccccccccccccc
-cctcccgagccgagccacccgtca
-ggggggggggggggggggggggg
-gttattaataataacttatcatca
-`))
+	tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
+	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"), 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: &taglib, skipOOO: true}
-	tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-gttattaataataacttatcatca
-cccccccccccccccccccc
-ggagaactgtgctccgccttcaga
-ggggggggggggggggggggggg
-gactctagcagagtggccagccac
-`))
+	tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
+	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"), 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: &taglib, skipOOO: true}
-	tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-ggagaactgtgctccgccttcaga
-cccccccccccccccccccc
-gactctagcagagtggccagccac
-ggggggggggggggggggggggg
-acacatgctagcgcgtcggggtgg
-`))
+	tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
+	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"), 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: &taglib, skipOOO: true}
-	tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-ggagaactgtgctccgccttcaga
-cccccccccccccccccccc
-acacatgctagcgcgtcggggtgg
-ggggggggggggggggggggggg
-acacatgctagcgcgtcggggtgg
-ggggggggggggggggggggggg
-gactctagcagagtggccagccac
-`))
+	tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
+	tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+		s.tag[0]+
+		"cccccccccccccccccccc\n"+
+		s.tag[1]+
+		"ggggggggggggggggggggggg\n"+
+		s.tag[1]+
+		"ggggggggggggggggggggggg\n"+
+		s.tag[2]+
+		"\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: &taglib, skipOOO: true}
-	tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-ggagaactgtgctccgccttcaga
-cccccccccccccccccccc
-acacatgctagcgcgtcggggtgg
-ggggggggggggggggggggggg
-cctcccgagccgagccacccgtca
-ggggggggggggggggggggggg
-ggagaactgtgctccgccttcaga
-ggggggggggggggggggggggg
-gttattaataataacttatcatca
-`))
+	tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
+	tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+		s.tag[0]+
+		"cccccccccccccccccccc\n"+
+		s.tag[1]+
+		"ggggggggggggggggggggggg\n"+
+		s.tag[3]+
+		"ggggggggggggggggggggggg\n"+
+		s.tag[0]+
+		"ggggggggggggggggggggggg\n"+
+		s.tag[4]+
+		"\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: &taglib, skipOOO: true}
-	tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-ggagaactgtgctccgccttcaga
-cccccccccccccccccccc
-acacatgctagcgcgtcggggtgg
-ggggggggggggggggggggggg
-cctcccgagccgagccacccgtca
-`))
+	tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
+	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"), matchAllChromosomes, false)
 	c.Assert(err, check.IsNil)
 	c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {3, 1}}})
 }