refs #17996
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
"net/http"
_ "net/http/pprof"
"os"
"net/http"
_ "net/http/pprof"
"os"
"runtime"
"sort"
"strings"
"runtime"
"sort"
"strings"
+ matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
+ if err != nil {
+ err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
+ return 1
+ }
+
taglen := -1
DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
if len(ent.TagSet) > 0 {
taglen := -1
DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
if len(ent.TagSet) > 0 {
}
}
for _, cg := range ent.CompactGenomes {
}
}
for _, cg := range ent.CompactGenomes {
- cgnames = append(cgnames, cg.Name)
+ if matchGenome.MatchString(cg.Name) {
+ cgnames = append(cgnames, cg.Name)
+ }
}
for _, tv := range ent.TileVariants {
if tv.Ref {
}
for _, tv := range ent.TileVariants {
if tv.Ref {
err = fmt.Errorf("tagset not found")
return 1
}
err = fmt.Errorf("tagset not found")
return 1
}
+ if len(cgnames) == 0 {
+ err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
+ return 1
+ }
seq[tv.Tag] = variants
}
for _, cg := range ent.CompactGenomes {
seq[tv.Tag] = variants
}
for _, cg := range ent.CompactGenomes {
+ if matchGenome.MatchString(cg.Name) {
+ cgs[cg.Name] = cg
+ }