[ViewVC] Annotation of: gclib/scripts/fqcount

#!/bin/tcsh -f
if ("x"$1 == 'x-h') then
 echo "Usage: fqcount [-M] <fastq_input>"
 echo ""
 echo "Count the number of reads in a fastq file"
 echo ""
 echo "Use -M to get the 'real' count if the duplicate reads were collapsed" 
 echo "and reads have the '_xN' suffix"
 exit 1
 endif
if ( "x"$1 == 'x-M' ) then
 shift
 perl -e '$n=0; while (<>) { if (m/^\@/ && m/_x(\d+)$/) {$n+=$1} } print $n."\n"' $1
 exit
endif
set n=`wc -l $1`
@ n /= 4
echo $n
Revision:	24
Committed:	Tue Jul 26 21:46:39 2011 UTC (13 years, 6 months ago) by gpertea
File size:	448 byte(s)
Log Message:
Line	File contents
1	#!/bin/tcsh -f
2	if ("x"$1 == 'x-h') then
3	echo "Usage: fqcount [-M] <fastq_input>"
4	echo ""
5	echo "Count the number of reads in a fastq file"
6	echo ""
7	echo "Use -M to get the 'real' count if the duplicate reads were collapsed"
8	echo "and reads have the '_xN' suffix"
9	exit 1
10	endif
11	if ( "x"$1 == 'x-M' ) then
12	shift
13	perl -e '$n=0; while (<>) { if (m/^\@/ && m/_x(\d+)$/) {$n+=$1} } print $n."\n"' $1
14	exit
15	endif
16	set n=`wc -l $1`
17	@ n /= 4
18	echo $n