Skip input files that aren't needed because -max-tag.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

diff --git a/slicenumpy.go b/slicenumpy.go
index 0cc9896b59a35dd6645c48617413a9d59a882e26..cb218041efbf503c2e67c306e525137015467628 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -8,6 +8,7 @@ import (
        "bufio"
        "bytes"
        "encoding/gob"
+       "errors"
        "flag"
        "fmt"
        "io"
@@ -363,6 +364,7 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
        throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
        throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
        log.Info("generating annotations and numpy matrix for each slice")
+       var errSkip = errors.New("skip infile")
        var done int64
        for infileIdx, infile := range infiles {
                infileIdx, infile := infileIdx, infile
@@ -400,6 +402,9 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                        seq[tv.Tag] = variants
                                }
                                for _, cg := range ent.CompactGenomes {
+                                       if cmd.filter.MaxTag >= 0 && cg.StartTag > tagID(cmd.filter.MaxTag) {
+                                               return errSkip
+                                       }
                                        if !matchGenome.MatchString(cg.Name) {
                                                continue
                                        }
@@ -413,7 +418,9 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                }
                                return nil
                        })
-                       if err != nil {
+                       if err == errSkip {
+                               return nil
+                       } else if err != nil {
                                return err
                        }
                        tagstart := cgs[cmd.cgnames[0]].StartTag