tools/etc/checkbam.sh

   1 #!/bin/bash
   2
   3 if [ x"$1" = x"" ]; then
   4    echo "Usage: $0 <outfile> [find_path(.)]"
   5    exit
   6 fi
   7
   8 if [ x"$2" = x"" ]; then
   9    TOFIND="."
  10 else
  11    TOFIND="$2"
  12 fi
  13 TOFIND=`readlink -nf ${TOFIND}`
  14
  15 date > $1
  16 echo "From [${TOFIND}] to [$1]:"
  17 echo "Find in [${TOFIND}]" >> $1
  18
  19 find -L ${TOFIND} -name '*.bam' | while read a;
  20  do echo -n "Checking [$a] ...";
  21     RES=`gzip -t "$a" 2>&1`;
  22     RETVAL=$?;
  23     if [ "${RETVAL}" -ne "0" ]; then
  24        echo -e "\b\b\b\b:Error=${RETVAL}.${RES}"
  25        echo "[e${RETVAL}] ${a}${RES}" >> $1
  26     else
  27        echo -e "\b\b\b\b:OK."
  28        echo "[ok] ${a}" >> $1
  29     fi;
  30  done
  31