Problem indexing multiple bed files

[mvdbeek]

Hi there,

I can't manage to index more than 1 file. I am trying this with a single-line bed file like this:

chr2L   450388  451555

$ giggle index -o test_idx9  -i a.bed.gz b.bed.gz
Indexed 1 intervals.

(a.bed.gz is a copy of b.bed.gz, but only 1 interval seems to be indexed) Consequently the same thing happens when I try to index a directory full of sorted and bgzip'ed bed files.

Is there anything I'm doing wrong ? I'm working off the master branch, but the docker container also seems to have the same issue. Any help would be much appreciated.

[ryanlayer]

put those bed files in their own directory, then use a wildcard to pass in the path.

mkdir bed_files mv a.bed.gz b.bed.gz bed_files giggle index -o test_idx9 -i "bed_files/*.bed.gz" -s -f

On Tue, Apr 17, 2018 at 10:26 AM, Marius van den Beek < notifications@github.com> wrote:

Hi there,

I can't manage to index more than 1 file. I am trying this with a single-line bed file like this:

chr2L 450388 451555

$ giggle index -o test_idx9 -i a.bed.gz b.bed.gz Indexed 1 intervals.

(a.bed.gz is a copy of b.bed.gz, but only 1 interval seems to be indexed:) Consequently the same thing happens when I try to index a directory full of sorted and bgzip'ed bed files.

Is there anything I'm doing wrong ? I'm working off the master branch, but the docker container also seems to have the same issue. Any help would be much appreciated.

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-- Ryan Layer

[mvdbeek]

Thanks, the quotes made the difference here. I guess it'd be more intuitive if those weren't required, but now I see it in the readme as well.