Add CalledBases to stats.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

diff --git a/stats.go b/stats.go
index 518cd132ac2adeb45aedd14dd1d8bbb433c1bb5e..a02fef701d6cf1dc671f2699ac46519f3ed0b15a 100644 (file)
--- a/stats.go
+++ b/stats.go
@@ -119,6 +119,7 @@ func (cmd *stats) RunCommand(prog string, args []string, stdin io.Reader, stdout
 func (cmd *stats) doStats(input io.Reader, 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
@@ -129,6 +130,7 @@ func (cmd *stats) doStats(input io.Reader, output io.Writer) error {
 
        var tagSet [][]byte
        var tagPlacements []int
+       tileVariantCalls := map[tileLibRef]int{}
        dec := gob.NewDecoder(bufio.NewReaderSize(input, 1<<26))
        for {
                var ent LibraryEntry
@@ -147,25 +149,18 @@ 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
                                }
                        }
@@ -175,6 +170,21 @@ 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)
                }
        }
        for id, p := range tagPlacements {