X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/761c4fd02d57e4e8c1190a94a3956e9de9f643df..ff2b46988b3e6c076766283325bb5ac04ab753f3:/tilelib.go

diff --git a/tilelib.go b/tilelib.go
index cfe91fb49f..8c88956b97 100644
--- a/tilelib.go
+++ b/tilelib.go
@@ -3,39 +3,267 @@ package main
 import (
 	"bufio"
 	"bytes"
+	"context"
+	"encoding/gob"
+	"fmt"
 	"io"
-	"log"
+	"regexp"
+	"runtime"
+	"sort"
+	"strings"
 	"sync"
+	"sync/atomic"
 
+	log "github.com/sirupsen/logrus"
 	"golang.org/x/crypto/blake2b"
 )
 
-type tileVariantID int32 // 1-based
+type tileVariantID uint16 // 1-based
 
 type tileLibRef struct {
-	tag     tagID
-	variant tileVariantID
+	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 {
-	taglib  *tagLibrary
-	variant [][][blake2b.Size256]byte
+	retainNoCalls       bool
+	skipOOO             bool
+	retainTileSequences bool
+
+	taglib         *tagLibrary
+	variant        [][][blake2b.Size256]byte
+	refseqs        map[string]map[string][]tileLibRef
+	compactGenomes map[string][]tileVariantID
 	// count [][]int
-	// seq map[[blake2b.Size]byte][]byte
-	variants int
+	seq      map[[blake2b.Size256]byte][]byte
+	variants int64
+	// if non-nil, write out any tile variants added while tiling
+	encoder *gob.Encoder
+
+	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).Variant
+	}
+	return nil
+}
+
+func (tilelib *tileLibrary) loadCompactGenomes(cgs []CompactGenome, variantmap map[tileLibRef]tileVariantID, onLoadGenome func(CompactGenome)) 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 onLoadGenome != nil {
+				onLoadGenome(cg)
+			}
+			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.Debugf("loadCompactSequences: %d", len(cseqs))
+	for _, cseq := range cseqs {
+		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
+			}
+		}
+	}
+	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
+	}
+	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.
+//
+// If onLoadGenome is non-nil, call it on each CompactGenome entry.
+func (tilelib *tileLibrary) LoadGob(ctx context.Context, rdr io.Reader, gz bool, onLoadGenome func(CompactGenome)) 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, onLoadGenome)
+	if err != nil {
+		return err
+	}
+	err = tilelib.loadCompactSequences(cseqs, variantmap)
+	if err != nil {
+		return err
+	}
+	return nil
+}
 
-	mtx sync.Mutex
+type importStats struct {
+	InputFile              string
+	InputLabel             string
+	InputLength            int
+	InputCoverage          int
+	PathLength             int
+	DroppedOutOfOrderTiles int
 }
 
-func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq, error) {
+func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader, matchChromosome *regexp.Regexp) (tileSeq, []importStats, error) {
 	ret := tileSeq{}
 	type jobT struct {
 		label string
 		fasta []byte
 	}
-	todo := make(chan jobT)
+	todo := make(chan jobT, 1)
 	scanner := bufio.NewScanner(rdr)
 	go func() {
 		defer close(todo)
@@ -43,72 +271,320 @@ func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq,
 		var seqlabel string
 		for scanner.Scan() {
 			buf := scanner.Bytes()
-			if len(buf) == 0 || buf[0] == '>' {
-				todo <- jobT{seqlabel, fasta}
-				seqlabel, fasta = string(buf[1:]), nil
-				log.Printf("%s %s reading fasta", filelabel, seqlabel)
+			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 {
 				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.Printf("%s %s tiling", filelabel, job.label)
-		var path []tileLibRef
-		tilestart := -1        // position in fasta of tile that ends here
-		tiletagid := tagID(-1) // tag id starting tile that ends here
-		tilelib.taglib.FindAll(job.fasta, func(id tagID, pos, taglen int) {
-			if tilestart >= 0 {
-				path = append(path, tilelib.getRef(tiletagid, job.fasta[tilestart:pos+taglen]))
-			}
-			tilestart = pos
-			tiletagid = id
+		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})
 		})
-		if tiletagid >= 0 {
-			path = append(path, tilelib.getRef(tiletagid, job.fasta[tilestart:]))
+		totalFoundTags += len(found)
+		if len(found) == 0 {
+			log.Warnf("%s %s no tags found", filelabel, job.label)
+		}
+
+		skipped := 0
+		if tilelib.skipOOO {
+			log.Infof("%s %s keeping longest increasing subsequence", filelabel, job.label)
+			keep := longestIncreasingSubsequence(len(found), func(i int) int { return int(found[i].tagid) })
+			for i, x := range keep {
+				found[i] = found[x]
+			}
+			skipped = len(found) - len(keep)
+			found = found[:len(keep)]
 		}
-		ret[job.label] = path
-		log.Printf("%s %s tiled with path len %d", filelabel, job.label, len(path))
+
+		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])
+				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 skipped-out-of-order %d", filelabel, job.label, len(job.fasta), basesIn, len(path), lowquality, skipped)
+		stats = append(stats, importStats{
+			InputFile:              filelabel,
+			InputLabel:             job.label,
+			InputLength:            len(job.fasta),
+			InputCoverage:          basesIn,
+			PathLength:             len(path),
+			DroppedOutOfOrderTiles: skipped,
+		})
+
+		totalPathLen += len(path)
 	}
-	return ret, scanner.Err()
+	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() int {
-	tilelib.mtx.Lock()
-	defer tilelib.mtx.Unlock()
-	return tilelib.variants
+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) tileLibRef {
-	for _, b := range seq {
-		if b != 'a' && b != 'c' && b != 'g' && b != 't' {
-			// return "tile not found" if seq has any
-			// no-calls
-			return tileLibRef{tag: tag}
+	dropSeq := false
+	if !tilelib.retainNoCalls {
+		for _, b := range seq {
+			if b != 'a' && b != 'c' && b != 'g' && b != 't' {
+				dropSeq = true
+				break
+			}
 		}
 	}
-	tilelib.mtx.Lock()
-	defer tilelib.mtx.Unlock()
-	// if tilelib.seq == nil {
-	// 	tilelib.seq = map[[blake2b.Size]byte][]byte{}
-	// }
-	if tilelib.variant == nil {
-		tilelib.variant = make([][][blake2b.Size256]byte, tilelib.taglib.Len())
-	}
 	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 {
-			return tileLibRef{tag: tag, variant: tileVariantID(i + 1)}
+			vlock.Unlock()
+			return tileLibRef{Tag: tag, Variant: tileVariantID(i + 1)}
 		}
 	}
-	tilelib.variants++
+	atomic.AddInt64(&tilelib.variants, 1)
 	tilelib.variant[tag] = append(tilelib.variant[tag], seqhash)
-	// tilelib.seq[seqhash] = append([]byte(nil), seq...)
-	return tileLibRef{tag: tag, variant: tileVariantID(len(tilelib.variant[tag]))}
+	variant := tileVariantID(len(tilelib.variant[tag]))
+	vlock.Unlock()
+
+	if tilelib.retainTileSequences && !dropSeq {
+		tilelib.mtx.Lock()
+		if tilelib.seq == nil {
+			tilelib.seq = map[[blake2b.Size256]byte][]byte{}
+		}
+		tilelib.seq[seqhash] = append([]byte(nil), seq...)
+		tilelib.mtx.Unlock()
+	}
+
+	if tilelib.encoder != nil {
+		saveSeq := seq
+		if dropSeq {
+			// Save the hash, but not the sequence
+			saveSeq = nil
+		}
+		tilelib.encoder.Encode(LibraryEntry{
+			TileVariants: []TileVariant{{
+				Tag:      tag,
+				Variant:  variant,
+				Blake2b:  seqhash,
+				Sequence: saveSeq,
+			}},
+		})
+	}
+	return tileLibRef{Tag: tag, Variant: variant}
+}
+
+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.seq[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")
+	for _, cg := range tilelib.compactGenomes {
+		for idx, variant := range cg {
+			cg[idx] = remap[tagID(idx/2)][variant]
+		}
+	}
+	for _, refcs := range tilelib.refseqs {
+		for _, refseq := range refcs {
+			for i, tv := range refseq {
+				refseq[i].Variant = remap[tv.Tag][tv.Variant]
+			}
+		}
+	}
+	log.Print("Tidy: done")
+}
+
+func countBases(seq []byte) int {
+	n := 0
+	for _, c := range seq {
+		if isbase[c] {
+			n++
+		}
+	}
+	return n
 }