run_sim_add_gfa_weights_sync-mg.sh

#!/bin/bash
. ${CONFIG:-$QDIR/config_illumina.sh}

# Adds weights using minigraph to align and amend the GFA

gfa=$1
query=$2

# Shred the FASTA file into small bits, simulating sequencing
echo === Shredding genome $query
shred_fa=$query.shred.fa
shred.pl -s 1 -l $shred_len -e $shred_err -d $shred_depth $query > $shred_fa

# Assemble and add these to the shredded input so we map both
eval syncasm $syncasm_opts $shred_fa
awk '/^S/ {printf(">%s\n",$2);print $3}' syncasm.asm.utg.gfa > $query.asm.fa
(cat $shred_fa; for i in `seq 1 30`; do cat $query.asm.fa; done) > $query.frags.fa

# Length specific minigraph options.  Long-read vs short-read
if [ $shred_len -gt 500 ]
then
    mg_opts="-x lr -w 15 -l 100 -d 100 -m 50,40 -n 5,5"
else
    mg_opts="-x sr"
fi
mg_opts="$mg_opts -j 0.01 --cov ${MINIGRAPH_OPTS}"

# Run minigraph to get a GFA
eval minigraph $mg_opts $gfa $query.frags.fa 2>mg.err > $query.mg

# Quantise dc:f field to kmer-count by multplying up the length.
# For edges we use it as EC direct, but in both cases it must be integer.
tag_gfa_mg.pl $query.mg > $query.gfa