readChecksum_MT.sh

#!/bin/bash

function logmsg(){
  echo -e "$1" >&2
}

READS=$1
NUMCPUS=12

if [ "$READS" == "" ]; then
  logmsg "Gets a checksum from a fastq.gz or a fastq file";
  logmsg "Usage: $0 file.fastq.gz";
  exit 1;
fi;

IS_GZIP=$(file $READS| grep gzip)

if [ "$IS_GZIP" == "" ]; then
  CAT="cat"
else
  CAT="zcat"
fi

# 1. cat the file to perl
# 2. keep only the seq and qual
# 3. sort
# 4. sha256sum
# 5. remove any whitespace and the dash from the sha256sum stdin printout
CHECKSUM=$($CAT $READS |\
            perl -Mthreads -e '
                               my $i=0;
                               while(<>){
                                 $seq=<>; 
                                 <>; 
                                 $qual=<>; 
                                 print "$seq$qual";
                               }' |\
            sort | sha256sum |\
            perl -lane 's/^\s+|\s+$//; s/\s+.*$//; print;'
          );

echo -e "$READS\t$CHECKSUM";