JohnLonginotto

yup = 0
b = 'AATTCCGGAATT'
p = set([b])
for x in range(0,len(b)):
    for x_val in ['A','C','G','T']:
        for y in range(0,len(b)):
            for y_val in ['A','C','G','T']:
                temp = list(b)
                temp[x],temp[y] = x_val,y_val
                p.add( ''.join(temp) )

JohnLonginotto

#!/usr/bin/perl
use strict;

open( IN_P1, "/Users/John/Desktop/ENCFF001LCU.fq" ) or die "File not found";
$| = 1;
my $yup = 0;
my $barcode1 = 'AATTCCGGAATT';
my $barcode1_regex = make_barcode_fragments( $barcode1 );

while ( defined( my $firstp1 = <IN_P1> ) ) {

JohnLonginotto

[Fri Apr 29 21:29:39 CEST 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar INPUT=[/home/kong/Haiying/Projects/Melanoma/Primary/ILSE530X_B20/Lock/Picard/T15520.sorted.sam] OUTPUT=/home/kong/Haiying/Projects/Melanoma/Primary/ILS
E530X_B20/Lock/Picard/T15520.dedupped.bam METRICS_FILE=/home/kong/Haiying/Projects/Melanoma/Primary/ILSE530X_B20/Lock/Picard/T15520.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true    MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGA
R=true BLOCK_SIZE=100000 DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as nu
meric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Fri Apr 29 21:29:39 CEST 2016] Executing as kong@hpc19 on Linux 3.2.53-1.e