explainSamFlag

#!/bin/bash
#
# Dirty utility script to convert a SAM bitwise flag from decimal
# to binary representation, pad with zeros and then interpret
# what each bit means
#
# An online tool to do this is at
# http://picard.sourceforge.net/explain-flags.html
#
# See also:
# http://ppotato.wordpress.com/2010/08/25/samtool-bitwise-flag-paired-reads/
# http://seqanswers.com/forums/showthread.php?t=2301
#

if [[ $# -eq 0 ]]; then
  echo Explain SAM flags in plain English
  echo ==================================
  echo
  echo Convert a decimal SAM flag to binary representation and
  echo print explanation of each bit.
  echo See also http://picard.sourceforge.net/explain-flags.html
  echo ""
  echo "Usage:  <flag_value>"
  echo ""
fi

function isset() {
  if [ "$1" == "1" ] ; then
    echo "YES $2"
  else
    echo "    $2"
  fi
}
if [ -z "$1" ] ; then
  echo "No decimal flag value supplied"
  exit 1
fi
echo Decimal flag = "$1"
#
# Convert decimal to binary
bin=$(echo "ibase=10; obase=2; $1" | bc)
#
# Pad with zeros
# FIXME This is horrible!
pad=12
len=$(echo "$bin" | wc -c)
while [ "$len" -lt $pad ] ; do
  bin="0$bin"
  len=$(echo "$bin" | wc -c)
done
echo Binary equivalent = "$bin"
echo
#
# Reverse
bin=$(echo "$bin" | rev)
#
# Explain
echo Explanation:
echo ============
isset "${bin:0:1}" "read paired (1)"
isset "${bin:1:1}" "read mapped in proper pair (2)"
isset "${bin:2:1}" "read unmapped (4)"
isset "${bin:3:1}" "mate unmapped (8)"
isset "${bin:4:1}" "read reverse strand (16)"
isset "${bin:5:1}" "mate reverse strand (32)"
isset "${bin:6:1}" "first in pair (64)"
isset "${bin:7:1}" "second in pair (128)"
isset "${bin:8:1}" "not primary alignment (256)"
isset "${bin:9:1}" "read fails platform/vendor quality checks (512)"
isset "${bin:10:1}" "read is PCR or optical duplicate (1024)"
isset "${bin:11:1}" "secondary alignment (2048)"