// Copyright (C) The Lightning Authors. All rights reserved.
//
// SPDX-License-Identifier: AGPL-3.0
package lightning
import (
"bufio"
"bytes"
"context"
"encoding/gob"
"fmt"
"io"
"os"
"regexp"
"runtime"
"sort"
"strings"
"sync"
"sync/atomic"
"github.com/klauspost/pgzip"
log "github.com/sirupsen/logrus"
"golang.org/x/crypto/blake2b"
)
type tileVariantID uint16 // 1-based
type tileLibRef struct {
Tag tagID
Variant tileVariantID
}
type tileSeq map[string][]tileLibRef
func (tseq tileSeq) Variants() ([]tileVariantID, int, int) {
maxtag := 0
for _, refs := range tseq {
for _, ref := range refs {
if maxtag < int(ref.Tag) {
maxtag = int(ref.Tag)
}
}
}
vars := make([]tileVariantID, maxtag+1)
var kept, dropped int
for _, refs := range tseq {
for _, ref := range refs {
if vars[int(ref.Tag)] != 0 {
dropped++
} else {
kept++
}
vars[int(ref.Tag)] = ref.Variant
}
}
return vars, kept, dropped
}
type tileLibrary struct {
retainNoCalls bool
skipOOO bool
retainTileSequences bool
useDups bool
taglib *tagLibrary
variant [][][blake2b.Size256]byte
refseqs map[string]map[string][]tileLibRef
compactGenomes map[string][]tileVariantID
seq2 map[[2]byte]map[[blake2b.Size256]byte][]byte
seq2lock map[[2]byte]sync.Locker
variants int64
// if non-nil, write out any tile variants added while tiling
encoder *gob.Encoder
// set Ref flag when writing new variants to encoder
encodeRef bool
onAddTileVariant func(libref tileLibRef, hash [blake2b.Size256]byte, seq []byte) error
onAddGenome func(CompactGenome) error
onAddRefseq func(CompactSequence) error
mtx sync.RWMutex
vlock []sync.Locker
}
func (tilelib *tileLibrary) loadTagSet(newtagset [][]byte) error {
// Loading a tagset means either passing it through to the
// output (if it's the first one we've seen), or just ensuring
// it doesn't disagree with what we already have.
if len(newtagset) == 0 {
return nil
}
tilelib.mtx.Lock()
defer tilelib.mtx.Unlock()
if tilelib.taglib == nil || tilelib.taglib.Len() == 0 {
tilelib.taglib = &tagLibrary{}
err := tilelib.taglib.setTags(newtagset)
if err != nil {
return err
}
if tilelib.encoder != nil {
err = tilelib.encoder.Encode(LibraryEntry{
TagSet: newtagset,
})
if err != nil {
return err
}
}
} else if tilelib.taglib.Len() != len(newtagset) {
return fmt.Errorf("cannot merge libraries with differing tagsets")
} else {
current := tilelib.taglib.Tags()
for i := range newtagset {
if !bytes.Equal(newtagset[i], current[i]) {
return fmt.Errorf("cannot merge libraries with differing tagsets")
}
}
}
return nil
}
func (tilelib *tileLibrary) loadTileVariants(tvs []TileVariant, variantmap map[tileLibRef]tileVariantID) error {
for _, tv := range tvs {
// Assign a new variant ID (unique across all inputs)
// for each input variant.
variantmap[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence, tv.Ref).Variant
}
return nil
}
func (tilelib *tileLibrary) loadCompactGenomes(cgs []CompactGenome, variantmap map[tileLibRef]tileVariantID) error {
log.Debugf("loadCompactGenomes: %d", len(cgs))
var wg sync.WaitGroup
errs := make(chan error, 1)
for _, cg := range cgs {
wg.Add(1)
cg := cg
go func() {
defer wg.Done()
for i, variant := range cg.Variants {
if len(errs) > 0 {
return
}
if variant == 0 {
continue
}
tag := tagID(i / 2)
newvariant, ok := variantmap[tileLibRef{Tag: tag, Variant: variant}]
if !ok {
err := fmt.Errorf("oops: genome %q has variant %d for tag %d, but that variant was not in its library", cg.Name, variant, tag)
select {
case errs <- err:
default:
}
return
}
// log.Tracef("loadCompactGenomes: cg %s tag %d variant %d => %d", cg.Name, tag, variant, newvariant)
cg.Variants[i] = newvariant
}
if tilelib.onAddGenome != nil {
err := tilelib.onAddGenome(cg)
if err != nil {
select {
case errs <- err:
default:
}
return
}
}
if tilelib.encoder != nil {
err := tilelib.encoder.Encode(LibraryEntry{
CompactGenomes: []CompactGenome{cg},
})
if err != nil {
select {
case errs <- err:
default:
}
return
}
}
if tilelib.compactGenomes != nil {
tilelib.mtx.Lock()
defer tilelib.mtx.Unlock()
tilelib.compactGenomes[cg.Name] = cg.Variants
}
}()
}
wg.Wait()
go close(errs)
return <-errs
}
func (tilelib *tileLibrary) loadCompactSequences(cseqs []CompactSequence, variantmap map[tileLibRef]tileVariantID) error {
log.Infof("loadCompactSequences: %d todo", len(cseqs))
for _, cseq := range cseqs {
log.Infof("loadCompactSequences: checking %s", cseq.Name)
for _, tseq := range cseq.TileSequences {
for i, libref := range tseq {
if libref.Variant == 0 {
// No variant (e.g., import
// dropped tiles with
// no-calls) = no translation.
continue
}
v, ok := variantmap[libref]
if !ok {
return fmt.Errorf("oops: CompactSequence %q has variant %d for tag %d, but that variant was not in its library", cseq.Name, libref.Variant, libref.Tag)
}
tseq[i].Variant = v
}
}
if tilelib.encoder != nil {
if err := tilelib.encoder.Encode(LibraryEntry{
CompactSequences: []CompactSequence{cseq},
}); err != nil {
return err
}
}
if tilelib.onAddRefseq != nil {
err := tilelib.onAddRefseq(cseq)
if err != nil {
return err
}
}
log.Infof("loadCompactSequences: checking %s done", cseq.Name)
}
tilelib.mtx.Lock()
defer tilelib.mtx.Unlock()
if tilelib.refseqs == nil {
tilelib.refseqs = map[string]map[string][]tileLibRef{}
}
for _, cseq := range cseqs {
tilelib.refseqs[cseq.Name] = cseq.TileSequences
}
log.Info("loadCompactSequences: done")
return nil
}
func allFiles(path string, re *regexp.Regexp) ([]string, error) {
var files []string
f, err := open(path)
if err != nil {
return nil, err
}
defer f.Close()
fis, err := f.Readdir(-1)
if err != nil {
return []string{path}, nil
}
for _, fi := range fis {
if fi.Name() == "." || fi.Name() == ".." {
continue
} else if child := path + "/" + fi.Name(); fi.IsDir() {
add, err := allFiles(child, re)
if err != nil {
return nil, err
}
files = append(files, add...)
} else if re == nil || re.MatchString(child) {
files = append(files, child)
}
}
sort.Strings(files)
return files, nil
}
var matchGobFile = regexp.MustCompile(`\.gob(\.gz)?$`)
func (tilelib *tileLibrary) LoadDir(ctx context.Context, path string) error {
log.Infof("LoadDir: walk dir %s", path)
files, err := allFiles(path, matchGobFile)
if err != nil {
return err
}
ctx, cancel := context.WithCancel(ctx)
defer cancel()
var mtx sync.Mutex
allcgs := make([][]CompactGenome, len(files))
allcseqs := make([][]CompactSequence, len(files))
allvariantmap := map[tileLibRef]tileVariantID{}
errs := make(chan error, len(files))
log.Infof("LoadDir: read %d files", len(files))
for fileno, path := range files {
fileno, path := fileno, path
go func() {
f, err := open(path)
if err != nil {
errs <- err
return
}
defer f.Close()
defer log.Infof("LoadDir: finished reading %s", path)
var variantmap = map[tileLibRef]tileVariantID{}
var cgs []CompactGenome
var cseqs []CompactSequence
err = DecodeLibrary(f, strings.HasSuffix(path, ".gz"), func(ent *LibraryEntry) error {
if ctx.Err() != nil {
return ctx.Err()
}
if len(ent.TagSet) > 0 {
mtx.Lock()
if tilelib.taglib == nil || tilelib.taglib.Len() != len(ent.TagSet) {
// load first set of tags, or
// report mismatch if 2 sets
// have different #tags.
if err := tilelib.loadTagSet(ent.TagSet); err != nil {
mtx.Unlock()
return err
}
}
mtx.Unlock()
}
for _, tv := range ent.TileVariants {
variantmap[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = tilelib.getRef(tv.Tag, tv.Sequence, tv.Ref).Variant
}
cgs = append(cgs, ent.CompactGenomes...)
cseqs = append(cseqs, ent.CompactSequences...)
return nil
})
allcgs[fileno] = cgs
allcseqs[fileno] = cseqs
mtx.Lock()
defer mtx.Unlock()
for k, v := range variantmap {
allvariantmap[k] = v
}
errs <- err
}()
}
for range files {
err := <-errs
if err != nil {
return err
}
}
log.Info("LoadDir: loadCompactGenomes")
var flatcgs []CompactGenome
for _, cgs := range allcgs {
flatcgs = append(flatcgs, cgs...)
}
err = tilelib.loadCompactGenomes(flatcgs, allvariantmap)
if err != nil {
return err
}
log.Info("LoadDir: loadCompactSequences")
var flatcseqs []CompactSequence
for _, cseqs := range allcseqs {
flatcseqs = append(flatcseqs, cseqs...)
}
err = tilelib.loadCompactSequences(flatcseqs, allvariantmap)
if err != nil {
return err
}
log.Info("LoadDir done")
return nil
}
func (tilelib *tileLibrary) WriteDir(dir string) error {
ntilefiles := 128
nfiles := ntilefiles + len(tilelib.refseqs)
files := make([]*os.File, nfiles)
for i := range files {
f, err := os.OpenFile(fmt.Sprintf("%s/library.%04d.gob.gz", dir, i), os.O_CREATE|os.O_WRONLY, 0666)
if err != nil {
return err
}
defer f.Close()
files[i] = f
}
bufws := make([]*bufio.Writer, nfiles)
for i := range bufws {
bufws[i] = bufio.NewWriterSize(files[i], 1<<26)
}
zws := make([]*pgzip.Writer, nfiles)
for i := range zws {
zws[i] = pgzip.NewWriter(bufws[i])
defer zws[i].Close()
}
encoders := make([]*gob.Encoder, nfiles)
for i := range encoders {
encoders[i] = gob.NewEncoder(zws[i])
}
cgnames := make([]string, 0, len(tilelib.compactGenomes))
for name := range tilelib.compactGenomes {
cgnames = append(cgnames, name)
}
sort.Strings(cgnames)
refnames := make([]string, 0, len(tilelib.refseqs))
for name := range tilelib.refseqs {
refnames = append(refnames, name)
}
sort.Strings(refnames)
log.Infof("WriteDir: writing %d files", nfiles)
ctx, cancel := context.WithCancel(context.Background())
defer cancel()
errs := make(chan error, nfiles)
for start := range files {
start := start
go func() {
err := encoders[start].Encode(LibraryEntry{TagSet: tilelib.taglib.Tags()})
if err != nil {
errs <- err
return
}
if refidx := start - ntilefiles; refidx >= 0 {
// write each ref to its own file
// (they seem to load very slowly)
name := refnames[refidx]
errs <- encoders[start].Encode(LibraryEntry{CompactSequences: []CompactSequence{{
Name: name,
TileSequences: tilelib.refseqs[name],
}}})
return
}
for i := start; i < len(cgnames); i += ntilefiles {
err := encoders[start].Encode(LibraryEntry{CompactGenomes: []CompactGenome{{
Name: cgnames[i],
Variants: tilelib.compactGenomes[cgnames[i]],
}}})
if err != nil {
errs <- err
return
}
}
tvs := []TileVariant{}
for tag := start; tag < len(tilelib.variant) && ctx.Err() == nil; tag += ntilefiles {
tvs = tvs[:0]
for idx, hash := range tilelib.variant[tag] {
tvs = append(tvs, TileVariant{
Tag: tagID(tag),
Variant: tileVariantID(idx + 1),
Blake2b: hash,
Sequence: tilelib.hashSequence(hash),
})
}
err := encoders[start].Encode(LibraryEntry{TileVariants: tvs})
if err != nil {
errs <- err
return
}
}
errs <- nil
}()
}
for range files {
err := <-errs
if err != nil {
return err
}
}
log.Info("WriteDir: flushing")
for i := range zws {
err := zws[i].Close()
if err != nil {
return err
}
err = bufws[i].Flush()
if err != nil {
return err
}
err = files[i].Close()
if err != nil {
return err
}
}
log.Info("WriteDir: done")
return nil
}
// Load library data from rdr. Tile variants might be renumbered in
// the process; in that case, genomes variants will be renumbered to
// match.
func (tilelib *tileLibrary) LoadGob(ctx context.Context, rdr io.Reader, gz bool) error {
cgs := []CompactGenome{}
cseqs := []CompactSequence{}
variantmap := map[tileLibRef]tileVariantID{}
err := DecodeLibrary(rdr, gz, func(ent *LibraryEntry) error {
if ctx.Err() != nil {
return ctx.Err()
}
if err := tilelib.loadTagSet(ent.TagSet); err != nil {
return err
}
if err := tilelib.loadTileVariants(ent.TileVariants, variantmap); err != nil {
return err
}
cgs = append(cgs, ent.CompactGenomes...)
cseqs = append(cseqs, ent.CompactSequences...)
return nil
})
if err != nil {
return err
}
if ctx.Err() != nil {
return ctx.Err()
}
err = tilelib.loadCompactGenomes(cgs, variantmap)
if err != nil {
return err
}
err = tilelib.loadCompactSequences(cseqs, variantmap)
if err != nil {
return err
}
return nil
}
func (tilelib *tileLibrary) dump(out io.Writer) {
printTV := func(tag int, variant tileVariantID) {
if variant < 1 {
fmt.Fprintf(out, " -")
} else if tag >= len(tilelib.variant) {
fmt.Fprintf(out, " (!tag=%d)", tag)
} else if int(variant) > len(tilelib.variant[tag]) {
fmt.Fprintf(out, " (tag=%d,!variant=%d)", tag, variant)
} else {
fmt.Fprintf(out, " %x", tilelib.variant[tag][variant-1][:8])
}
}
for refname, refseqs := range tilelib.refseqs {
for seqname, seq := range refseqs {
fmt.Fprintf(out, "ref %s %s", refname, seqname)
for _, libref := range seq {
printTV(int(libref.Tag), libref.Variant)
}
fmt.Fprintf(out, "\n")
}
}
for name, cg := range tilelib.compactGenomes {
fmt.Fprintf(out, "cg %s", name)
for tag, variant := range cg {
printTV(tag/2, variant)
}
fmt.Fprintf(out, "\n")
}
}
type importStats struct {
InputFile string
InputLabel string
InputLength int
InputCoverage int
PathLength int
DroppedRepeatedTags int
DroppedOutOfOrderTags int
}
func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader, matchChromosome *regexp.Regexp, isRef bool) (tileSeq, []importStats, error) {
ret := tileSeq{}
type jobT struct {
label string
fasta []byte
}
todo := make(chan jobT, 1)
scanner := bufio.NewScanner(rdr)
scanner.Buffer(make([]byte, 256), 1<<29) // 512 MiB, in case fasta does not have line breaks
go func() {
defer close(todo)
var fasta []byte
var seqlabel string
for scanner.Scan() {
buf := scanner.Bytes()
if len(buf) > 0 && buf[0] == '>' {
todo <- jobT{seqlabel, append([]byte(nil), fasta...)}
seqlabel, fasta = strings.SplitN(string(buf[1:]), " ", 2)[0], fasta[:0]
log.Debugf("%s %s reading fasta", filelabel, seqlabel)
} else if len(buf) > 0 && buf[0] == '#' {
// ignore testdata comment
} else {
fasta = append(fasta, bytes.ToLower(buf)...)
}
}
todo <- jobT{seqlabel, fasta}
}()
type foundtag struct {
pos int
tagid tagID
}
found := make([]foundtag, 2000000)
path := make([]tileLibRef, 2000000)
totalFoundTags := 0
totalPathLen := 0
skippedSequences := 0
taglen := tilelib.taglib.TagLen()
var stats []importStats
for job := range todo {
if len(job.fasta) == 0 {
continue
} else if !matchChromosome.MatchString(job.label) {
skippedSequences++
continue
}
log.Debugf("%s %s tiling", filelabel, job.label)
found = found[:0]
tilelib.taglib.FindAll(job.fasta, func(tagid tagID, pos, taglen int) {
found = append(found, foundtag{pos: pos, tagid: tagid})
})
totalFoundTags += len(found)
if len(found) == 0 {
log.Warnf("%s %s no tags found", filelabel, job.label)
}
droppedDup := 0
if !tilelib.useDups {
// Remove any tags that appeared more than once
dup := map[tagID]bool{}
for _, ft := range found {
_, dup[ft.tagid] = dup[ft.tagid]
}
dst := 0
for _, ft := range found {
if !dup[ft.tagid] {
found[dst] = ft
dst++
}
}
droppedDup = len(found) - dst
log.Infof("%s %s dropping %d non-unique tags", filelabel, job.label, droppedDup)
found = found[:dst]
}
droppedOOO := 0
if tilelib.skipOOO {
keep := longestIncreasingSubsequence(len(found), func(i int) int { return int(found[i].tagid) })
for i, x := range keep {
found[i] = found[x]
}
droppedOOO = len(found) - len(keep)
log.Infof("%s %s dropping %d out-of-order tags", filelabel, job.label, droppedOOO)
found = found[:len(keep)]
}
log.Infof("%s %s getting %d librefs", filelabel, job.label, len(found))
throttle := &throttle{Max: runtime.NumCPU()}
path = path[:len(found)]
var lowquality int64
for i, f := range found {
i, f := i, f
throttle.Acquire()
go func() {
defer throttle.Release()
var startpos, endpos int
if i == 0 {
startpos = 0
} else {
startpos = f.pos
}
if i == len(found)-1 {
endpos = len(job.fasta)
} else {
endpos = found[i+1].pos + taglen
}
path[i] = tilelib.getRef(f.tagid, job.fasta[startpos:endpos], isRef)
if countBases(job.fasta[startpos:endpos]) != endpos-startpos {
atomic.AddInt64(&lowquality, 1)
}
}()
}
throttle.Wait()
log.Infof("%s %s copying path", filelabel, job.label)
pathcopy := make([]tileLibRef, len(path))
copy(pathcopy, path)
ret[job.label] = pathcopy
basesIn := countBases(job.fasta)
log.Infof("%s %s fasta in %d coverage in %d path len %d low-quality %d", filelabel, job.label, len(job.fasta), basesIn, len(path), lowquality)
stats = append(stats, importStats{
InputFile: filelabel,
InputLabel: job.label,
InputLength: len(job.fasta),
InputCoverage: basesIn,
PathLength: len(path),
DroppedOutOfOrderTags: droppedOOO,
DroppedRepeatedTags: droppedDup,
})
totalPathLen += len(path)
}
log.Printf("%s tiled with total path len %d in %d sequences (skipped %d sequences that did not match chromosome regexp, skipped %d out-of-order tags)", filelabel, totalPathLen, len(ret), skippedSequences, totalFoundTags-totalPathLen)
return ret, stats, scanner.Err()
}
func (tilelib *tileLibrary) Len() int64 {
return atomic.LoadInt64(&tilelib.variants)
}
// Return a tileLibRef for a tile with the given tag and sequence,
// adding the sequence to the library if needed.
func (tilelib *tileLibrary) getRef(tag tagID, seq []byte, usedByRef bool) tileLibRef {
dropSeq := false
if !tilelib.retainNoCalls {
for _, b := range seq {
if b != 'a' && b != 'c' && b != 'g' && b != 't' {
dropSeq = true
break
}
}
}
seqhash := blake2b.Sum256(seq)
var vlock sync.Locker
tilelib.mtx.RLock()
if len(tilelib.vlock) > int(tag) {
vlock = tilelib.vlock[tag]
}
tilelib.mtx.RUnlock()
if vlock != nil {
vlock.Lock()
for i, varhash := range tilelib.variant[tag] {
if varhash == seqhash {
vlock.Unlock()
return tileLibRef{Tag: tag, Variant: tileVariantID(i + 1)}
}
}
vlock.Unlock()
} else {
tilelib.mtx.Lock()
if tilelib.variant == nil && tilelib.taglib != nil {
tilelib.variant = make([][][blake2b.Size256]byte, tilelib.taglib.Len())
tilelib.vlock = make([]sync.Locker, tilelib.taglib.Len())
for i := range tilelib.vlock {
tilelib.vlock[i] = new(sync.Mutex)
}
}
if int(tag) >= len(tilelib.variant) {
oldlen := len(tilelib.vlock)
for i := 0; i < oldlen; i++ {
tilelib.vlock[i].Lock()
}
// If we haven't seen the tag library yet (as
// in a merge), tilelib.taglib.Len() is
// zero. We can still behave correctly, we
// just need to expand the tilelib.variant and
// tilelib.vlock slices as needed.
if int(tag) >= cap(tilelib.variant) {
// Allocate 2x capacity.
newslice := make([][][blake2b.Size256]byte, int(tag)+1, (int(tag)+1)*2)
copy(newslice, tilelib.variant)
tilelib.variant = newslice[:int(tag)+1]
newvlock := make([]sync.Locker, int(tag)+1, (int(tag)+1)*2)
copy(newvlock, tilelib.vlock)
tilelib.vlock = newvlock[:int(tag)+1]
} else {
// Use previously allocated capacity,
// avoiding copy.
tilelib.variant = tilelib.variant[:int(tag)+1]
tilelib.vlock = tilelib.vlock[:int(tag)+1]
}
for i := oldlen; i < len(tilelib.vlock); i++ {
tilelib.vlock[i] = new(sync.Mutex)
}
for i := 0; i < oldlen; i++ {
tilelib.vlock[i].Unlock()
}
}
vlock = tilelib.vlock[tag]
tilelib.mtx.Unlock()
}
vlock.Lock()
for i, varhash := range tilelib.variant[tag] {
if varhash == seqhash {
vlock.Unlock()
return tileLibRef{Tag: tag, Variant: tileVariantID(i + 1)}
}
}
atomic.AddInt64(&tilelib.variants, 1)
tilelib.variant[tag] = append(tilelib.variant[tag], seqhash)
variant := tileVariantID(len(tilelib.variant[tag]))
vlock.Unlock()
if tilelib.retainTileSequences && !dropSeq {
seqCopy := append([]byte(nil), seq...)
if tilelib.seq2 == nil {
tilelib.mtx.Lock()
if tilelib.seq2 == nil {
tilelib.seq2lock = map[[2]byte]sync.Locker{}
m := map[[2]byte]map[[blake2b.Size256]byte][]byte{}
var k [2]byte
for i := 0; i < 256; i++ {
k[0] = byte(i)
for j := 0; j < 256; j++ {
k[1] = byte(j)
m[k] = map[[blake2b.Size256]byte][]byte{}
tilelib.seq2lock[k] = &sync.Mutex{}
}
}
tilelib.seq2 = m
}
tilelib.mtx.Unlock()
}
var k [2]byte
copy(k[:], seqhash[:])
locker := tilelib.seq2lock[k]
locker.Lock()
tilelib.seq2[k][seqhash] = seqCopy
locker.Unlock()
}
saveSeq := seq
if dropSeq {
// Save the hash, but not the sequence
saveSeq = nil
}
if tilelib.encoder != nil {
tilelib.encoder.Encode(LibraryEntry{
TileVariants: []TileVariant{{
Tag: tag,
Ref: usedByRef,
Variant: variant,
Blake2b: seqhash,
Sequence: saveSeq,
}},
})
}
if tilelib.onAddTileVariant != nil {
tilelib.onAddTileVariant(tileLibRef{tag, variant}, seqhash, saveSeq)
}
return tileLibRef{Tag: tag, Variant: variant}
}
func (tilelib *tileLibrary) hashSequence(hash [blake2b.Size256]byte) []byte {
var partition [2]byte
copy(partition[:], hash[:])
return tilelib.seq2[partition][hash]
}
func (tilelib *tileLibrary) TileVariantSequence(libref tileLibRef) []byte {
if libref.Variant == 0 || len(tilelib.variant) <= int(libref.Tag) || len(tilelib.variant[libref.Tag]) < int(libref.Variant) {
return nil
}
return tilelib.hashSequence(tilelib.variant[libref.Tag][libref.Variant-1])
}
// Tidy deletes unreferenced tile variants and renumbers variants so
// more common variants have smaller IDs.
func (tilelib *tileLibrary) Tidy() {
log.Print("Tidy: compute inref")
inref := map[tileLibRef]bool{}
for _, refseq := range tilelib.refseqs {
for _, librefs := range refseq {
for _, libref := range librefs {
inref[libref] = true
}
}
}
log.Print("Tidy: compute remap")
remap := make([][]tileVariantID, len(tilelib.variant))
throttle := throttle{Max: runtime.NumCPU() + 1}
for tag, oldvariants := range tilelib.variant {
tag, oldvariants := tagID(tag), oldvariants
if tag%1000000 == 0 {
log.Printf("Tidy: tag %d", tag)
}
throttle.Acquire()
go func() {
defer throttle.Release()
uses := make([]int, len(oldvariants))
for _, cg := range tilelib.compactGenomes {
for phase := 0; phase < 2; phase++ {
cgi := int(tag)*2 + phase
if cgi < len(cg) && cg[cgi] > 0 {
uses[cg[cgi]-1]++
}
}
}
// Compute desired order of variants:
// neworder[x] == index in oldvariants that
// should move to position x.
neworder := make([]int, len(oldvariants))
for i := range neworder {
neworder[i] = i
}
sort.Slice(neworder, func(i, j int) bool {
if cmp := uses[neworder[i]] - uses[neworder[j]]; cmp != 0 {
return cmp > 0
} else {
return bytes.Compare(oldvariants[neworder[i]][:], oldvariants[neworder[j]][:]) < 0
}
})
// Replace tilelib.variant[tag] with a new
// re-ordered slice of hashes, and make a
// mapping from old to new variant IDs.
remaptag := make([]tileVariantID, len(oldvariants)+1)
newvariants := make([][blake2b.Size256]byte, 0, len(neworder))
for _, oldi := range neworder {
if uses[oldi] > 0 || inref[tileLibRef{Tag: tag, Variant: tileVariantID(oldi + 1)}] {
newvariants = append(newvariants, oldvariants[oldi])
remaptag[oldi+1] = tileVariantID(len(newvariants))
}
}
tilelib.variant[tag] = newvariants
remap[tag] = remaptag
}()
}
throttle.Wait()
// Apply remap to genomes and reference sequences, so they
// refer to the same tile variants using the changed IDs.
log.Print("Tidy: apply remap")
var wg sync.WaitGroup
for _, cg := range tilelib.compactGenomes {
cg := cg
wg.Add(1)
go func() {
defer wg.Done()
for idx, variant := range cg {
cg[idx] = remap[tagID(idx/2)][variant]
}
}()
}
for _, refcs := range tilelib.refseqs {
for _, refseq := range refcs {
refseq := refseq
wg.Add(1)
go func() {
defer wg.Done()
for i, tv := range refseq {
refseq[i].Variant = remap[tv.Tag][tv.Variant]
}
}()
}
}
wg.Wait()
log.Print("Tidy: done")
}
func countBases(seq []byte) int {
n := 0
for _, c := range seq {
if isbase[c] {
n++
}
}
return n
}