Accept double file extensions (sample-id.1.fa.fa.gz).

No issue #

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

diff --git a/import.go b/import.go
index 9bc336af107acf0c4c3ffea9f95f39de0a4b3a40..20058dc8a9f184dbc5c88c9d32cd32399dd3da34 100644 (file)
--- a/import.go
+++ b/import.go
@@ -281,8 +281,8 @@ func (cmd *importer) loadTagLibrary() (*tagLibrary, error) {
 
 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)?$`)
        fastaFilenameRe  = regexp.MustCompile(`\.fa(sta)?(\.gz)?$`)
 )
 
@@ -347,32 +347,32 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                if fasta1FilenameRe.MatchString(infile) {
                        todo <- func() error {
                                defer phases.Done()
-                               log.Printf("%s starting", infile)
+                               log.Printf("%s (sample.1) starting tiling", infile)
                                defer log.Printf("%s done", infile)
                                tseqs, stats, err := cmd.tileFasta(tilelib, infile, false)
                                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
                        }
-                       infile2 := fasta1FilenameRe.ReplaceAllString(infile, `.2.fa$1$2`)
+                       infile2 := fasta1FilenameRe.ReplaceAllString(infile, `.2.fa$1$2$4`)
                        todo <- func() error {
                                defer phases.Done()
-                               log.Printf("%s starting", infile2)
+                               log.Printf("%s (sample.2) starting tiling", infile2)
                                defer log.Printf("%s done", infile2)
                                tseqs, stats, err := cmd.tileFasta(tilelib, infile2, false)
                                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()
-                               log.Printf("%s starting", infile)
+                               log.Printf("%s (reference) starting tiling", infile)
                                defer log.Printf("%s done", infile)
                                tseqs, stats, err := cmd.tileFasta(tilelib, infile, true)
                                allstats[idx*2] = stats
@@ -383,7 +383,7 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                                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()