--prefix not used

[webbchen]

Dear developers

I ran:

/path/to/apps/fixchr/bin/fixchr \
-c /path/to/some_comparative_genomics/syri_Hp1_to_pm1.delta.m.coords \
-r /path/to/some_comparative_genomics/assembly_pm1_v1_upper.fasta \
-q /path/to/some_comparative_genomics/Hp1.fasta \
--contig_size 5000 \
--dir /path/to/some_comparative_genomics/ \
--prefix Hp1_to_pm1

but the output had no prefix whatsoever.

ref.filtered.fa
qry.filtered.fa
homologous_strand_corrected.pdf
homologous_strand_corrected_alignments.txt
homologous_alignments.txt
homologous.pdf
input.pdf
input_alignments.txt

Which is harmless, unless you run more than one instance.

Kind regards,

AWebb

[mnshgl0110]

Thanks for pointing this out. It seems that I have not implemented this yet. I will try to add this when I get some time. Pull requests to add this feature are also welcome.

[hyBio]

“ ref.filtered.fa qry.filtered.fa homologous_strand_corrected.pdf homologous_strand_corrected_alignments.txt homologous_alignments.txt homologous.pdf input.pdf input_alignments.txt ” Which file is the input file that needs to be used for the syri -c, I found that the files returned by fixchr will have a header line, which will cause the syri to report an error, and I may need to delete them manually, can this be avoided in the code? like this: $$$ awk '!($1 ~ /^[0-9]+$/) {print}' homologous_strand_corrected_alignments.txt aStart aEnd bStart bEnd aLen bLen iden aDir bDir aChr bChr cigar

[mnshgl0110]

@hyBio Please check this: https://github.com/schneebergerlab/fixchr/issues/9#issuecomment-1822672004