Closed jeromekelleher closed 10 years ago
Do people use colons in filenames?
Colons are used in cortex to separate multiple input paths e.g. -2 in1.fa:in2.fa
and cases where you also want to specify an output path -2 in1.fa:in2.fa:dir/out
.
I've just committed a fix (b4e966d) for colons in single file paths (e.g. the case you use -1 A:2.fasta
), but you'll still have issues if you use colons in -2
cases etc. Workaround is to rename your file or create a symlink.
Using a filename that contains a colon as input results in an error:
$ ./ctx31 build -k 31 -sA -1 A:2.fasta out [07 Jul 2014 13:34:59-Zid][cmd] ./ctx31 build -k 31 -sA -1 A:2.fasta out [07 Jul 2014 13:34:59-Zid][cwd] /home/jk/work/wt/prg/hla_graph [07 Jul 2014 13:34:59-Zid][version] ctx=v0.0.3-29-gf1407a7 zlib=1.2.7 htslib=0.2.0-rc8-6-gd49dfa6 ASSERTS=ON CHECKS=ON k=3..31 [src/basic/async_read_io.c:51] Error asyncio_task_parse(): Expected -1
[07 Jul 2014 13:34:59-Zid] Fatal Error