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Fix off-by-one in chunk ranges #320

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Fix off-by-one in chunk ranges #320

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0cceb4a
fix off-by-one issue in chunk ranges
tkchafin Sep 11, 2024
fc737b2
made chunk size an argument
tkchafin Sep 11, 2024
d8a76e6
fix typo
tkchafin Sep 11, 2024
ca4096e
linting
tkchafin Sep 11, 2024
7f08a9d
remove chunk size as argument
tkchafin Sep 17, 2024
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11 changes: 6 additions & 5 deletions bin/generate_cram_csv.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -12,24 +12,25 @@ chunk_cram() {
local cram=$1
local chunkn=$2
local outcsv=$3
local chunksize=10000
realcram=$(readlink -f ${cram})
realcrai=$(readlink -f ${cram}.crai)
local rgline=$(samtools view -H "${realcram}" | grep "@RG" | sed 's/\t/\\t/g' | sed "s/'//g")
local ncontainers=$(zcat "${realcrai}" | wc -l)
local base=$(basename "${realcram}" .cram)
local from=0
local to=10000

local to=$((chunksize - 1))

while [ $to -lt $ncontainers ]; do
echo "${realcram},${realcrai},${from},${to},${base},${chunkn},${rgline}" >> $outcsv
from=$((to + 1))
((to += 10000))
to=$((to + chunksize))
((chunkn++))
done

if [ $from -le $ncontainers ]; then
echo "${realcram},${realcrai},${from},${ncontainers},${base},${chunkn},${rgline}" >> $outcsv
if [ $from -lt $ncontainers ]; then
to=$((ncontainers - 1))
echo "${realcram},${realcrai},${from},${to},${base},${chunkn},${rgline}" >> $outcsv
((chunkn++))
fi

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