Installation from scratch fail with file examples

[fingels]

Hi,

I installed (today) ggcat following the instructions provided in the README section, on a Linux machine, with installation of rust / nightly toolchain, cloning the sources and so on.

I tried to build the colored graph on the examples provided with a file color_mapping.in :

A1	sal1.fa
A2	sal2.fa
A3	sal3.fa

And running the command ggcat build -k 21 -c -d color_mapping.in gave me the following error :

Allocator initialized: mem: 2 GiB chunks: 8192 log2: 18
Using m: 10 with k: 21
Add index with color A1 => 0
Add index with color A2 => 1
Add index with color A3 => 2
Thread panicked at location: crates/io/src/sequences_stream/fasta.rs:15:14
Backtrace:    0: <unknown>
   1: <unknown>
   2: <unknown>
   3: <unknown>
   4: <unknown>
   5: <unknown>
   6: <unknown>
   7: <unknown>
   8: <unknown>
   9: <unknown>
  10: <unknown>
  11: <unknown>
  12: <unknown>
  13: <unknown>
  14: <unknown>
  15: <unknown>
  16: <unknown>
  17: __libc_start_call_main
             at ./csu/../sysdeps/nptl/libc_start_call_main.h:58:16
  18: __libc_start_main_impl
             at ./csu/../csu/libc-start.c:392:3
  19: <unknown>

I was able to replicate the error on separate Linux machines.

[Guilucand]

Hi, the problem is that the files are not found, since the paths inside the mapping file were (wrongly) intended as relative to the current working directory. I fixed the problem, and now the relative paths inside a mapping file are adjusted using the mapping file path.

[fingels]

Thanks, it worked perfectly.