Configurable chromosome name pattern.

[lightning.git] / tilelib.go

diff --git a/tilelib.go b/tilelib.go
index 5ad12e7228667024e562e12b8a6030f7fefac05a..12facfdb5f665226f5d1de0952d30ea5c7bb5181 100644 (file)
--- a/tilelib.go
+++ b/tilelib.go
@@ -7,6 +7,7 @@ import (
        "encoding/gob"
        "fmt"
        "io"
+       "regexp"
        "runtime"
        "sort"
        "strings"
@@ -255,7 +256,7 @@ type importStats struct {
        DroppedOutOfOrderTiles int
 }
 
-func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq, []importStats, error) {
+func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader, matchChromosome *regexp.Regexp) (tileSeq, []importStats, error) {
        ret := tileSeq{}
        type jobT struct {
                label string
@@ -293,7 +294,7 @@ func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq,
        for job := range todo {
                if len(job.fasta) == 0 {
                        continue
-               } else if strings.Contains(job.label, "_") {
+               } else if !matchChromosome.MatchString(job.label) {
                        skippedSequences++
                        continue
                }
@@ -373,7 +374,7 @@ func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq,
 
                totalPathLen += len(path)
        }
-       log.Printf("%s tiled with total path len %d in %d sequences (skipped %d sequences with '_' in name, skipped %d out-of-order tags)", filelabel, totalPathLen, len(ret), skippedSequences, totalFoundTags-totalPathLen)
+       log.Printf("%s tiled with total path len %d in %d sequences (skipped %d sequences that did not match chromosome regexp, skipped %d out-of-order tags)", filelabel, totalPathLen, len(ret), skippedSequences, totalFoundTags-totalPathLen)
        return ret, stats, scanner.Err()
 }