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mcveanlab / mccortex

De novo genome assembly and multisample variant calling
https://github.com/mcveanlab/mccortex/wiki
MIT License
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Bug: input file names containing colons not accepted #4

Closed jeromekelleher closed 10 years ago

jeromekelleher commented 10 years ago

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

noporpoise commented 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.