X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/7ebff453d609e6231a57ea831c31fe5374695550..79e0bd0ff72ae1759e8b780e5d8b61b09c9a0399:/stats.go

diff --git a/stats.go b/stats.go
index 62fb17d4fd..69e66da9a7 100644
--- a/stats.go
+++ b/stats.go
@@ -1,8 +1,11 @@
-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"
@@ -12,16 +15,17 @@ import (
 	"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 {
@@ -101,7 +105,7 @@ func (cmd *stats) RunCommand(prog string, args []string, stdin io.Reader, stdout
 	}
 
 	bufw := bufio.NewWriter(output)
-	err = cmd.doStats(input, bufw)
+	err = cmd.doStats(input, strings.HasSuffix(*inputFilename, ".gz"), bufw)
 	if err != nil {
 		return 1
 	}
@@ -116,9 +120,10 @@ func (cmd *stats) RunCommand(prog string, args []string, stdin io.Reader, stdout
 	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
@@ -129,15 +134,8 @@ func (cmd *stats) doStats(input io.Reader, output io.Writer) error {
 
 	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 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 {
@@ -147,25 +145,18 @@ func (cmd *stats) doStats(input io.Reader, output io.Writer) error {
 			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
 				}
 			}
@@ -175,7 +166,26 @@ func (cmd *stats) doStats(input io.Reader, output io.Writer) error {
 			} 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 {