Add -expand-regions flag.

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

diff --git a/exportnumpy.go b/exportnumpy.go
index 95ab3d08ce0e905a9b8ebbb913e0c99323ed8134..39663daa65c6c3b1977fa3d618e0a30bf15bfe7b 100644 (file)
--- a/exportnumpy.go
+++ b/exportnumpy.go
@@ -46,6 +46,7 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
        librefsFilename := flags.String("output-onehot2tilevar", "", "when using -one-hot, create csv `file` mapping column# to tag# and variant#")
        labelsFilename := flags.String("output-labels", "", "output `file` for genome labels csv")
        regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
+       expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
        onehot := flags.Bool("one-hot", false, "recode tile variants as one-hot")
        chunks := flags.Int("chunks", 1, "split output into `N` numpy files")
        cmd.filter.Flags(flags)
@@ -90,6 +91,7 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
                        "-output-onehot2tilevar", "/mnt/output/onehot2tilevar.csv",
                        "-output-labels", "/mnt/output/labels.csv",
                        "-regions", *regionsFilename,
+                       "-expand-regions", fmt.Sprintf("%d", *expandRegions),
                        "-max-variants", fmt.Sprintf("%d", cmd.filter.MaxVariants),
                        "-min-coverage", fmt.Sprintf("%f", cmd.filter.MinCoverage),
                        "-max-tag", fmt.Sprintf("%d", cmd.filter.MaxTag),
@@ -162,7 +164,7 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
        }
 
        log.Info("determining which tiles intersect given regions")
-       dropTiles, err := chooseTiles(tilelib, *regionsFilename)
+       dropTiles, err := chooseTiles(tilelib, *regionsFilename, *expandRegions)
        if err != nil {
                return 1
        }
@@ -321,7 +323,7 @@ func cgs2array(tilelib *tileLibrary, names []string, lowqual []map[tileVariantID
        return
 }
 
-func chooseTiles(tilelib *tileLibrary, regionsFilename string) (drop []bool, err error) {
+func chooseTiles(tilelib *tileLibrary, regionsFilename string, expandRegions int) (drop []bool, err error) {
        if regionsFilename == "" {
                return
        }
@@ -364,7 +366,7 @@ func chooseTiles(tilelib *tileLibrary, regionsFilename string) (drop []bool, err
                                return
                        }
                }
-               mask.Add(refseqname, start, end)
+               mask.Add(refseqname, start-expandRegions, end+expandRegions)
        }
        log.Print("chooseTiles: mask.Freeze")
        mask.Freeze()