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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,29 +1,82 @@ | ||
| #!/bin/bash | ||
| cram_path=$1 | ||
| chunkn=0 | ||
| for cram in ${cram_path}/*.cram; do | ||
| rgline=$(samtools view -H $cram|grep "RG"|sed 's/\t/\\t/g'|sed "s/'//g") | ||
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| crampath=$(readlink -f ${cram}) | ||
| # generate_cram_csv.sh | ||
| # ------------------- | ||
| # Generate a csv file describing the CRAM folder | ||
| # ><((((°> Y ><((((°> U ><((((°> M ><((((°> I ><((((°> | ||
| # Author = yy5 | ||
| # ><((((°> Y ><((((°> U ><((((°> M ><((((°> I ><((((°> | ||
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| ncontainers=$(zcat ${crampath}.crai|wc -l) | ||
| base=$(basename $cram .cram) | ||
| # Function to process chunking of a CRAM file | ||
| chunk_cram() { | ||
| local cram=$1 | ||
| local chunkn=$2 | ||
| local outcsv=$3 | ||
| realcram=$(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 | ||
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| from=0 | ||
| to=10000 | ||
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| while [ $to -lt $ncontainers ] | ||
| do | ||
| echo $crampath,${crampath}.crai,${from},${to},${base},${chunkn},${rgline} | ||
| from=$((to+1)) | ||
| ((to+=10000)) | ||
| while [ $to -lt $ncontainers ]; do | ||
| echo "${realcram},${realcrai},${from},${to},${base},${chunkn},${rgline}" >> $outcsv | ||
| from=$((to + 1)) | ||
| ((to += 10000)) | ||
| ((chunkn++)) | ||
| done | ||
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| if [ $from -le $ncontainers ] | ||
| then | ||
| echo $crampath,${crampath}.crai,${from},${ncontainers},${base},${chunkn},${rgline} | ||
| if [ $from -le $ncontainers ]; then | ||
| echo "${realcram},${realcrai},${from},${ncontainers},${base},${chunkn},${rgline}" >> $outcsv | ||
| ((chunkn++)) | ||
| fi | ||
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| echo $chunkn | ||
| } | ||
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| # Function to process a CRAM file | ||
| process_cram_file() { | ||
| local cram=$1 | ||
| local chunkn=$2 | ||
| local outcsv=$3 | ||
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| local read_groups=$(samtools view -H "$cram" | grep '@RG' | awk '{for(i=1;i<=NF;i++){if($i ~ /^ID:/){print substr($i,4)}}}') | ||
| local num_read_groups=$(echo "$read_groups" | wc -w) | ||
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| if [ "$num_read_groups" -gt 1 ]; then | ||
| # Multiple read groups: process each separately | ||
| for rg in $read_groups; do | ||
| local output_cram="$(basename "${cram%.cram}")_output_${rg}.cram" | ||
| samtools view -h -r "$rg" -o "$output_cram" "$cram" | ||
| samtools index "$output_cram" | ||
| chunkn=$(chunk_cram "$output_cram" "$chunkn" "$outcsv") | ||
| done | ||
| else | ||
| # Single read group or no read groups | ||
| chunkn=$(chunk_cram "$cram" "$chunkn" "$outcsv") | ||
| fi | ||
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| echo $chunkn | ||
| } | ||
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| # /\_/\ /\_/\ | ||
| # ( o.o ) main ( o.o ) | ||
| # > ^ < > ^ < | ||
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| # Check if cram_path is provided | ||
| if [ -z "$1" ]; then | ||
| echo "Usage: $0 <cram_path>" | ||
| exit 1 | ||
| fi | ||
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| cram_path=$1 | ||
| chunkn=0 | ||
| outcsv=$2 | ||
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| # Loop through each CRAM file in the specified directory. cram cannot be the synlinked cram | ||
| for cram in ${cram_path}/*.cram; do | ||
| realcram=$(readlink -f $cram) | ||
| chunkn=$(process_cram_file $realcram $chunkn $outcsv) | ||
| done |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -49,4 +49,3 @@ process SELFCOMP_SPLITFASTA { | |
| END_VERSIONS | ||
| """ | ||
| } | ||
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