For fixing FTDNA version 1 BAM files that incorrectly include a space in the QNAME field

fixFTDNAbam.sh

#!/bin/bash
#
# Fixes FTDNA BAM version 1 files so can be processed by standard bioinformatic tools.  
#  Applies only to Bigy files (not needed for Bigy2 or Bigy3)
#
# This is handled behind the scenes (automagically) by WGS Extract (in the next release)
# Simply a stand-alone. simple scenario script installation for demonstration purposes here
#
# Relies on htslib bgzip and samtools; along with wget, python rm, zip and unzip.

shopt -s nullglob
if [ $# -ne 1 ] ; then
  echo "Usage: $0 FTDNA_BAM_zip_file or file.bam"
  exit
elif [ ! -f "$1" ] ; then
  echo "$1 is not a file"
  exit
fi
file="$1"

ext=${file##*.}
case $ext in
zip)
  mkdir temp_for_BAM
  cd temp_for_BAM
  unzip ../"$1"
  file="*.bam"
  ;;
 bam)
   file="$1"
   ;;
 *)
   echo "Unknown file type: $1"
   exit
   ;;
 esac

wget https://github.com/WGSExtract/WGSExtract-Dev/blob/master/program/fixFTDNAbam.py
samtools view -h "$file" | python fixFTDNAbam.py | bgzip > new.bam
mv new.bam "$file"
samtools index "$file"
rm fixFTDNAvcf.py

case $ext in
zip)
  zip -f "../$1" "$file" "$file.bai"
  rm "$file" "$file.bai"y
  cd ..
  rmdir temp_for_BAM
  ;;
*)
  ;;
esac