-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
import (
"bufio"
- "encoding/gob"
"encoding/json"
"errors"
"flag"
"net/http"
_ "net/http/pprof"
"os"
+ "strings"
"git.arvados.org/arvados.git/sdk/go/arvados"
log "github.com/sirupsen/logrus"
)
-type stats struct {
+type statscmd struct {
debugUnplaced bool
}
-func (cmd *stats) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
+func (cmd *statscmd) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
var err error
defer func() {
if err != nil {
return 0
} else if err != nil {
return 2
+ } else if flags.NArg() > 0 {
+ err = fmt.Errorf("errant command line arguments after parsed flags: %v", flags.Args())
+ return 2
}
if *pprof != "" {
}
bufw := bufio.NewWriter(output)
- err = cmd.doStats(input, bufw)
+ err = cmd.doStats(input, strings.HasSuffix(*inputFilename, ".gz"), bufw)
if err != nil {
return 1
}
return 0
}
-func (cmd *stats) doStats(input io.Reader, output io.Writer) error {
+func (cmd *statscmd) doStats(input io.Reader, gz bool, output io.Writer) error {
var ret struct {
Genomes int
+ CalledBases []int64
Tags int
TagsPlacedNTimes []int // a[x]==y means there were y tags that placed x times
TileVariants int
var tagSet [][]byte
var tagPlacements []int
- dec := gob.NewDecoder(bufio.NewReaderSize(input, 1<<26))
- for {
- var ent LibraryEntry
- err := dec.Decode(&ent)
- if err == io.EOF {
- break
- } else if err != nil {
- return fmt.Errorf("gob decode: %w", err)
- }
+ tileVariantCalls := map[tileLibRef]int{}
+ err := DecodeLibrary(input, gz, func(ent *LibraryEntry) error {
ret.Genomes += len(ent.CompactGenomes)
ret.TileVariants += len(ent.TileVariants)
if len(ent.TagSet) > 0 {
ret.Tags = len(ent.TagSet)
tagSet = ent.TagSet
}
- for _, g := range ent.CompactGenomes {
- if need := (len(g.Variants)+1)/2 - len(tagPlacements); need > 0 {
- tagPlacements = append(tagPlacements, make([]int, need)...)
- }
- for idx, v := range g.Variants {
- if v > 0 {
- tagPlacements[idx/2]++
- }
- }
- }
for _, tv := range ent.TileVariants {
if need := 1 + len(tv.Sequence) - len(ret.VariantsBySize); need > 0 {
ret.VariantsBySize = append(ret.VariantsBySize, make([]int, need)...)
ret.NCVariantsBySize = append(ret.NCVariantsBySize, make([]int, need)...)
}
+ calls := 0
hasNoCalls := false
for _, b := range tv.Sequence {
- if b != 'a' && b != 'c' && b != 'g' && b != 't' {
+ if b == 'a' || b == 'c' || b == 'g' || b == 't' {
+ calls++
+ } else {
hasNoCalls = true
}
}
} else {
ret.VariantsBySize[len(tv.Sequence)]++
}
+
+ tileVariantCalls[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = calls
+ }
+ for _, g := range ent.CompactGenomes {
+ if need := (len(g.Variants)+1)/2 - len(tagPlacements); need > 0 {
+ tagPlacements = append(tagPlacements, make([]int, need)...)
+ }
+ calledBases := int64(0)
+ for idx, v := range g.Variants {
+ if v > 0 {
+ tagPlacements[idx/2]++
+ calledBases += int64(tileVariantCalls[tileLibRef{Tag: tagID(idx / 2), Variant: v}])
+ }
+ }
+ ret.CalledBases = append(ret.CalledBases, calledBases)
}
+ return nil
+ })
+ if err != nil {
+ return err
}
for id, p := range tagPlacements {
for len(ret.TagsPlacedNTimes) <= p {