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Fix some tests.
[lightning.git]
/
import.go
diff --git
a/import.go
b/import.go
index 79537347ee6f3fa6dfd32f69df00455cb456f477..20058dc8a9f184dbc5c88c9d32cd32399dd3da34 100644
(file)
--- a/
import.go
+++ b/
import.go
@@
-185,7
+185,7
@@
func (cmd *importer) runBatches(stdout io.Writer, inputs []string) error {
Client: arvadosClientFromEnv,
ProjectUUID: cmd.projectUUID,
APIAccess: true,
Client: arvadosClientFromEnv,
ProjectUUID: cmd.projectUUID,
APIAccess: true,
- RAM:
70
0000000000,
+ RAM:
35
0000000000,
VCPUs: 96,
Priority: cmd.priority,
KeepCache: 1,
VCPUs: 96,
Priority: cmd.priority,
KeepCache: 1,
@@
-234,7
+234,7
@@
func (cmd *importer) runBatches(stdout io.Writer, inputs []string) error {
return nil
}
return nil
}
-func (cmd *importer) tileFasta(tilelib *tileLibrary, infile string) (tileSeq, []importStats, error) {
+func (cmd *importer) tileFasta(tilelib *tileLibrary, infile string
, isRef bool
) (tileSeq, []importStats, error) {
var input io.ReadCloser
input, err := open(infile)
if err != nil {
var input io.ReadCloser
input, err := open(infile)
if err != nil {
@@
-249,7
+249,7
@@
func (cmd *importer) tileFasta(tilelib *tileLibrary, infile string) (tileSeq, []
}
defer input.Close()
}
}
defer input.Close()
}
- return tilelib.TileFasta(infile, input, cmd.matchChromosome)
+ return tilelib.TileFasta(infile, input, cmd.matchChromosome
, isRef
)
}
func (cmd *importer) loadTagLibrary() (*tagLibrary, error) {
}
func (cmd *importer) loadTagLibrary() (*tagLibrary, error) {
@@
-281,8
+281,8
@@
func (cmd *importer) loadTagLibrary() (*tagLibrary, error) {
var (
vcfFilenameRe = regexp.MustCompile(`\.vcf(\.gz)?$`)
var (
vcfFilenameRe = regexp.MustCompile(`\.vcf(\.gz)?$`)
- fasta1FilenameRe = regexp.MustCompile(`\.1\.fa(sta)?(\.gz)?$`)
- fasta2FilenameRe = regexp.MustCompile(`\.2\.fa(sta)?(\.gz)?$`)
+ fasta1FilenameRe = regexp.MustCompile(`\.1\.fa(sta)?(\.
fa(sta)?)?(\.
gz)?$`)
+ fasta2FilenameRe = regexp.MustCompile(`\.2\.fa(sta)?(\.
fa(sta)?)?(\.
gz)?$`)
fastaFilenameRe = regexp.MustCompile(`\.fa(sta)?(\.gz)?$`)
)
fastaFilenameRe = regexp.MustCompile(`\.fa(sta)?(\.gz)?$`)
)
@@
-347,34
+347,34
@@
func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
if fasta1FilenameRe.MatchString(infile) {
todo <- func() error {
defer phases.Done()
if fasta1FilenameRe.MatchString(infile) {
todo <- func() error {
defer phases.Done()
- log.Printf("%s
start
ing", infile)
+ log.Printf("%s
(sample.1) starting til
ing", infile)
defer log.Printf("%s done", infile)
defer log.Printf("%s done", infile)
- tseqs, stats, err := cmd.tileFasta(tilelib, infile)
+ tseqs, stats, err := cmd.tileFasta(tilelib, infile
, false
)
allstats[idx*2] = stats
var kept, dropped int
variants[0], kept, dropped = tseqs.Variants()
allstats[idx*2] = stats
var kept, dropped int
variants[0], kept, dropped = tseqs.Variants()
- log.Printf("%s found %d unique tags plus %d repeats", infile, kept, dropped)
+ log.Printf("%s
(sample.1)
found %d unique tags plus %d repeats", infile, kept, dropped)
return err
}
return err
}
- infile2 := fasta1FilenameRe.ReplaceAllString(infile, `.2.fa$1$2`)
+ infile2 := fasta1FilenameRe.ReplaceAllString(infile, `.2.fa$1$2
$4
`)
todo <- func() error {
defer phases.Done()
todo <- func() error {
defer phases.Done()
- log.Printf("%s
start
ing", infile2)
+ log.Printf("%s
(sample.2) starting til
ing", infile2)
defer log.Printf("%s done", infile2)
defer log.Printf("%s done", infile2)
- tseqs, stats, err := cmd.tileFasta(tilelib, infile2)
+ tseqs, stats, err := cmd.tileFasta(tilelib, infile2
, false
)
allstats[idx*2+1] = stats
var kept, dropped int
variants[1], kept, dropped = tseqs.Variants()
allstats[idx*2+1] = stats
var kept, dropped int
variants[1], kept, dropped = tseqs.Variants()
- log.Printf("%s found %d unique tags plus %d repeats", infile2, kept, dropped)
+ log.Printf("%s
(sample.2)
found %d unique tags plus %d repeats", infile2, kept, dropped)
return err
}
} else if fastaFilenameRe.MatchString(infile) {
todo <- func() error {
defer phases.Done()
defer phases.Done()
return err
}
} else if fastaFilenameRe.MatchString(infile) {
todo <- func() error {
defer phases.Done()
defer phases.Done()
- log.Printf("%s
start
ing", infile)
+ log.Printf("%s
(reference) starting til
ing", infile)
defer log.Printf("%s done", infile)
defer log.Printf("%s done", infile)
- tseqs, stats, err := cmd.tileFasta(tilelib, infile)
+ tseqs, stats, err := cmd.tileFasta(tilelib, infile
, true
)
allstats[idx*2] = stats
if err != nil {
return err
allstats[idx*2] = stats
if err != nil {
return err
@@
-383,7
+383,7
@@
func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
for _, tseq := range tseqs {
totlen += len(tseq)
}
for _, tseq := range tseqs {
totlen += len(tseq)
}
- log.Printf("%s tiled %d seqs, total len %d", infile, len(tseqs), totlen)
+ log.Printf("%s
(reference)
tiled %d seqs, total len %d", infile, len(tseqs), totlen)
if cmd.retainAfterEncoding {
tilelib.mtx.Lock()
if cmd.retainAfterEncoding {
tilelib.mtx.Lock()
@@
-448,7
+448,7
@@
func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
go close(todo)
var tileJobs sync.WaitGroup
var running int64
go close(todo)
var tileJobs sync.WaitGroup
var running int64
- for i := 0; i < runtime.GOMAXPROCS(-1)
*2
; i++ {
+ for i := 0; i < runtime.GOMAXPROCS(-1); i++ {
tileJobs.Add(1)
atomic.AddInt64(&running, 1)
go func() {
tileJobs.Add(1)
atomic.AddInt64(&running, 1)
go func() {
@@
-540,7
+540,7
@@
func (cmd *importer) tileGVCF(tilelib *tileLibrary, infile string, phase int) (t
return
}
defer consensus.Wait()
return
}
defer consensus.Wait()
- tileseq, stats, err = tilelib.TileFasta(fmt.Sprintf("%s phase %d", infile, phase+1), stdout, cmd.matchChromosome)
+ tileseq, stats, err = tilelib.TileFasta(fmt.Sprintf("%s phase %d", infile, phase+1), stdout, cmd.matchChromosome
, false
)
if err != nil {
return
}
if err != nil {
return
}