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// Copyright ©2015 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
package csi
import (
"bytes"
"testing"
"github.com/biogo/hts/bgzf"
"github.com/biogo/hts/bgzf/index"
"gopkg.in/check.v1"
)
func Test(t *testing.T) { check.TestingT(t) }
type S struct{}
var _ = check.Suite(&S{})
// conceptualCSIv1data is an uncompressed CSIv1 for the alignments in the BAM
// corresponding to:
//
// @HD VN:1.0 SO:coordinate
// @SQ SN:conceptual LN:134217728
// 60m66m:bin0 0 conceptual 62914561 40 6291456M * 0 0 * *
// 70m76m:bin2 0 conceptual 73400321 40 6291456M * 0 0 * *
// 73m75m:bin18 0 conceptual 76546049 40 2097152M * 0 0 * *
//
// This is a coordinate-translated version of the conceptual example in the
// SAM spec using binning as actually used by BAM rather than as presented.
/*
0x43, 0x53, 0x49, 0x01, // Index\1
0x0e, 0x00, 0x00, 0x00, // min_shift
0x05, 0x00, 0x00, 0x00, // depth
0x00, 0x00, 0x00, 0x00, // l_aux
// no aux
0x01, 0x00, 0x00, 0x00, // n_ref
0x02, 0x00, 0x00, 0x00, // n_bin
0x00, 0x00, 0x00, 0x00, // bin
0x00, 0x00, 0x65, 0x00, 0x00, 0x00, 0x00, 0x00, // loffset
0x01, 0x00, 0x00, 0x00, // n_chunk
0x00, 0x00, 0x65, 0x00, 0x00, 0x00, 0x00, 0x00, // chunk_beg {101,0}
0x00, 0x00, 0xe4, 0x00, 0x00, 0x00, 0x00, 0x00, // chunk_end {228,0}
// Not mentioned in the Index spec.
0x4a, 0x92, 0x00, 0x00, // bin - always 0x924a
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, // loffset
0x02, 0x00, 0x00, 0x00, // n_chunk - always 2
0x00, 0x00, 0x65, 0x00, 0x00, 0x00, 0x00, 0x00, // unmapped_beg
0x00, 0x00, 0xe4, 0x00, 0x00, 0x00, 0x00, 0x00, // unmapped_end
0x03, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, // mapped_count
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, // unmapped_count
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, // n_no_coor
*/
var conceptualCSIv1data = []byte{
0x43, 0x53, 0x49, 0x01, 0x0e, 0x00, 0x00, 0x00,
0x05, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x01, 0x00, 0x00, 0x00, 0x02, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x65, 0x00,
0x00, 0x00, 0x00, 0x00, 0x01, 0x00, 0x00, 0x00,
0x00, 0x00, 0x65, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0xe4, 0x00, 0x00, 0x00, 0x00, 0x00,
0x4a, 0x92, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x02, 0x00, 0x00, 0x00,
0x00, 0x00, 0x65, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0xe4, 0x00, 0x00, 0x00, 0x00, 0x00,
0x03, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
}
var chunkTests = []struct {
beg, end int
expect []bgzf.Chunk
}{
{
beg: 65000, end: 71000, // Index does not use tiles, so this is hit.
expect: []bgzf.Chunk{
{Begin: bgzf.Offset{File: 101, Block: 0}, End: bgzf.Offset{File: 228, Block: 0}},
},
},
{
beg: 77594624, end: 80740352, // 73m77m:bin2+bin18 - This is the equivalent to the given example.
expect: []bgzf.Chunk{
{Begin: bgzf.Offset{File: 101, Block: 0}, End: bgzf.Offset{File: 228, Block: 0}},
},
},
{
beg: 62914561, end: 68157440, // 60m65m:bin0+bin2
expect: []bgzf.Chunk{
{Begin: bgzf.Offset{File: 101, Block: 0}, End: bgzf.Offset{File: 228, Block: 0}},
},
},
{
beg: 72351744, end: 80740352, // 69m77m:bin0+bin2+18
expect: []bgzf.Chunk{
{Begin: bgzf.Offset{File: 101, Block: 0}, End: bgzf.Offset{File: 228, Block: 0}},
},
},
{
beg: 61865984, end: 80740352, // 59m77m:bin0+bin2+bin18
expect: []bgzf.Chunk{
{Begin: bgzf.Offset{File: 101, Block: 0}, End: bgzf.Offset{File: 228, Block: 0}},
},
},
{
beg: 80740352, end: 81788928, // 77m78m - Not in covered region, but Index does not use tiles, so this is hit.
expect: []bgzf.Chunk{
{Begin: bgzf.Offset{File: 101, Block: 0}, End: bgzf.Offset{File: 228, Block: 0}},
},
},
}
func (s *S) TestConceptualCSIv1(c *check.C) {
csi, err := ReadFrom(bytes.NewReader(conceptualCSIv1data))
c.Assert(err, check.Equals, nil)
for _, test := range chunkTests {
c.Check(csi.Chunks(0, test.beg, test.end), check.DeepEquals, test.expect,
check.Commentf("Unexpected result for [%d,%d).", test.beg, test.end),
)
}
stats, ok := csi.ReferenceStats(0)
c.Check(ok, check.Equals, true)
c.Check(stats, check.Equals, index.ReferenceStats{
Chunk: bgzf.Chunk{
Begin: bgzf.Offset{File: 101, Block: 0},
End: bgzf.Offset{File: 228, Block: 0},
},
Mapped: 3, Unmapped: 0})
unmapped, ok := csi.Unmapped()
c.Check(ok, check.Equals, true)
c.Check(unmapped, check.Equals, uint64(0))
}
// conceptualCSIv2data is an uncompressed CSIv1 for the alignments in the BAM
// corresponding to:
//
// @HD VN:1.0 SO:coordinate
// @SQ SN:conceptual LN:134217728
// 60m66m:bin0 0 conceptual 62914561 40 6291456M * 0 0 * *
// 70m76m:bin2 0 conceptual 73400321 40 6291456M * 0 0 * *
// 73m75m:bin18 0 conceptual 76546049 40 2097152M * 0 0 * *
//
// This is a coordinate-translated version of the conceptual example in the
// SAM spec using binning as actually used by BAM rather than as presented.
/*
0x43, 0x53, 0x49, 0x02, // Index\1
0x0e, 0x00, 0x00, 0x00, // min_shift
0x05, 0x00, 0x00, 0x00, // depth
0x00, 0x00, 0x00, 0x00, // l_aux
// no aux
0x01, 0x00, 0x00, 0x00, // n_ref
0x02, 0x00, 0x00, 0x00, // n_bin
0x00, 0x00, 0x00, 0x00, // bin
0x00, 0x00, 0x65, 0x00, 0x00, 0x00, 0x00, 0x00, // loffset
0x01, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, // n_rec
0x01, 0x00, 0x00, 0x00, // n_chunk
0x00, 0x00, 0x65, 0x00, 0x00, 0x00, 0x00, 0x00, // chunk_beg
0x00, 0x00, 0xe4, 0x00, 0x00, 0x00, 0x00, 0x00, // chunk_end
0x4a, 0x92, 0x00, 0x00, // bin
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, // loffset
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, // n_rec
0x02, 0x00, 0x00, 0x00, // n_chunk
0x00, 0x00, 0x65, 0x00, 0x00, 0x00, 0x00, 0x00, // unmapped_beg
0x00, 0x00, 0xe4, 0x00, 0x00, 0x00, 0x00, 0x00, // unmapped_end
0x03, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, // mapped_count
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, // unmapped_count
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
*/
var conceptualCSIv2data = []byte{
0x43, 0x53, 0x49, 0x02, 0x0e, 0x00, 0x00, 0x00,
0x05, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x01, 0x00, 0x00, 0x00, 0x02, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x65, 0x00,
0x00, 0x00, 0x00, 0x00, 0x01, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x01, 0x00, 0x00, 0x00,
0x00, 0x00, 0x65, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0xe4, 0x00, 0x00, 0x00, 0x00, 0x00,
0x4a, 0x92, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x02, 0x00, 0x00, 0x00,
0x00, 0x00, 0x65, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0xe4, 0x00, 0x00, 0x00, 0x00, 0x00,
0x03, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
}
func (s *S) TestConceptualCSIv2(c *check.C) {
csi, err := ReadFrom(bytes.NewReader(conceptualCSIv2data))
c.Assert(err, check.Equals, nil)
for _, test := range chunkTests {
c.Check(csi.Chunks(0, test.beg, test.end), check.DeepEquals, test.expect,
check.Commentf("Unexpected result for [%d,%d).", test.beg, test.end),
)
}
stats, ok := csi.ReferenceStats(0)
c.Check(ok, check.Equals, true)
c.Check(stats, check.Equals, index.ReferenceStats{
Chunk: bgzf.Chunk{
Begin: bgzf.Offset{File: 101, Block: 0},
End: bgzf.Offset{File: 228, Block: 0},
},
Mapped: 3, Unmapped: 0})
unmapped, ok := csi.Unmapped()
c.Check(ok, check.Equals, true)
c.Check(unmapped, check.Equals, uint64(0))
}
func uint64ptr(i uint64) *uint64 {
return &i
}
var csiTestData = []struct {
csi *Index
err error
}{
{
csi: &Index{
minShift: 14, depth: 5,
refs: []refIndex{
{
bins: []bin{
{
bin: 4681, left: bgzf.Offset{File: 98, Block: 0},
chunks: []bgzf.Chunk{
{Begin: bgzf.Offset{File: 98, Block: 0}, End: bgzf.Offset{File: 401, Block: 0}},
},
},
},
stats: &index.ReferenceStats{
Chunk: bgzf.Chunk{Begin: bgzf.Offset{File: 98, Block: 0}, End: bgzf.Offset{File: 401, Block: 0}},
Mapped: 8,
Unmapped: 1,
},
},
},
unmapped: uint64ptr(1),
isSorted: true,
},
err: nil,
},
{
csi: &Index{
minShift: 14, depth: 5,
refs: []refIndex{
{
bins: []bin{
{
bin: 4681, left: bgzf.Offset{File: 98, Block: 0},
chunks: []bgzf.Chunk{
{Begin: bgzf.Offset{File: 98, Block: 0}, End: bgzf.Offset{File: 401, Block: 0}},
},
},
},
stats: &index.ReferenceStats{
Chunk: bgzf.Chunk{Begin: bgzf.Offset{File: 98, Block: 0}, End: bgzf.Offset{File: 401, Block: 0}},
Mapped: 8,
Unmapped: 1,
},
},
},
unmapped: nil,
isSorted: true,
},
err: nil,
},
{
csi: &Index{
minShift: 14, depth: 5,
refs: []refIndex{
{
bins: []bin{
{
bin: 4681, left: bgzf.Offset{File: 98, Block: 0},
chunks: []bgzf.Chunk{
{Begin: bgzf.Offset{File: 98, Block: 0}, End: bgzf.Offset{File: 401, Block: 0}},
},
},
},
stats: nil,
},
},
unmapped: uint64ptr(1),
isSorted: true,
},
err: nil,
},
{
csi: &Index{
minShift: 14, depth: 5,
refs: []refIndex{
{
bins: []bin{
{
bin: 4681, left: bgzf.Offset{File: 98, Block: 0},
chunks: []bgzf.Chunk{
{Begin: bgzf.Offset{File: 98, Block: 0}, End: bgzf.Offset{File: 401, Block: 0}},
},
},
},
stats: nil,
},
},
unmapped: nil,
isSorted: true,
},
err: nil,
},
{
csi: &Index{
Auxilliary: []byte("Various commentary strings"),
minShift: 14, depth: 5,
refs: func() []refIndex {
idx := [86]refIndex{
23: {
bins: []bin{
{
bin: 0x2070,
chunks: []bgzf.Chunk{
{
Begin: bgzf.Offset{File: 0x1246, Block: 0x0},
End: bgzf.Offset{File: 0x1246, Block: 0x1cf9},
},
},
},
},
stats: &index.ReferenceStats{
Chunk: bgzf.Chunk{
Begin: bgzf.Offset{File: 0x1246, Block: 0x0},
End: bgzf.Offset{File: 0x1246, Block: 0x1cf9},
},
Mapped: 0, Unmapped: 0x1d,
},
},
24: {
bins: []bin{
{
bin: 0x124a,
chunks: []bgzf.Chunk{
{
Begin: bgzf.Offset{File: 0x1246, Block: 0x1cf9},
End: bgzf.Offset{File: 0x1246, Block: 0x401d},
},
},
},
},
stats: &index.ReferenceStats{
Chunk: bgzf.Chunk{
Begin: bgzf.Offset{File: 0x1246, Block: 0x1cf9},
End: bgzf.Offset{File: 0x1246, Block: 0x401d},
},
Mapped: 0, Unmapped: 0x25,
},
},
72: {
bins: []bin{
{
bin: 0x1253,
chunks: []bgzf.Chunk{
{
Begin: bgzf.Offset{File: 0x1246, Block: 0x401d},
End: bgzf.Offset{File: 0x1246, Block: 0x41f5},
},
},
},
},
stats: &index.ReferenceStats{
Chunk: bgzf.Chunk{
Begin: bgzf.Offset{File: 0x1246, Block: 0x401d},
End: bgzf.Offset{File: 0x1246, Block: 0x41f5},
},
Mapped: 0, Unmapped: 0x2,
},
},
}
return idx[:]
}(),
unmapped: uint64ptr(932),
isSorted: true,
},
err: nil,
},
}
func (s *S) TestCSIRoundtrip(c *check.C) {
for i, test := range csiTestData {
for test.csi.Version = 1; test.csi.Version <= 2; test.csi.Version++ {
var buf bytes.Buffer
c.Assert(WriteTo(&buf, test.csi), check.Equals, nil)
got, err := ReadFrom(&buf)
c.Assert(err, check.Equals, nil, check.Commentf("Test %d", i))
c.Check(got, check.DeepEquals, test.csi, check.Commentf("Test %d", i))
}
}
}
|
