Open ffinfo opened 8 years ago
@ffinfo, you can pipe into centrifuge-kreport
. That means one of the two following ways should work, depending on your shell:
gunzip -c centrifuge-out.gz | centrifuge-kreport -x IDX
# or, using an in-place file (with bash)
centrifuge-kreport -x IDX <(gunzip -c centrifuge-out.gz)
Can you try that?
Oh good, going to try this. Well let you know if this works. Maybe good to add this to the usage of the script/tool?
The first one does not work because centrifuge-kreport does not read from stdin. The second one is basicly a inline fifo pipe, this does work.
For usability it's might be a good thing to let the tool also accept input from stdin and directly from a .gz file.
Fixed the input from STDIN. Will add the feature to read directly from a gzipped file in the future.
It would be nice if the kreport script supports zipped input files. The output is now 1 line for each read/pair, this can become a very large file. Just piping from centrifuge to gzip is easy but kreport does not support this.