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Bug in mccortex join with --sort option #80

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@winni2k

Description

I think I have encountered a bug in mccortex join when I use it with the --sort output option. Here is what I mean:

echo -e '>1\nCCCGGG' > 1.fa
echo -e '>1\nCCCAAA' > 2.fa

mccortex 3 build -k 3 -s 1 -1 1.fa 1.ctx
mccortex 3 build -k 3 -s 2 -1 2.fa 2.ctx

## This works OK
mccortex 3 join -o isec.ctx -i 2.ctx 1.ctx

mccortex 3 view --kmers isec.ctx 2>/dev/null
# returns correct value:
# CCC 2 ........

rm isec.ctx

## This does not 
mccortex 3 join --sort -o isec.ctx -i 2.ctx 1.ctx 2>/dev/null

mccortex 3 view --kmers isec.ctx
# returns all kmers in 2.ctx with zero coverage and edges removed???:
# AAA 0 ........
# CAA 0 ........
# CCA 0 ........
# CCC 0 ........

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      Bug in `mccortex join` with --sort option · Issue #80 · mcveanlab/mccortex