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Description: Make the build reproducible
Author: Chris Lamb <lamby@debian.org>
Last-Update: 2016-10-08
Bug-Debian: https://bugs.debian.org/840140
--- fastx-toolkit-0.0.14.orig/scripts/fasta_clipping_histogram.pl
+++ fastx-toolkit-0.0.14/scripts/fasta_clipping_histogram.pl
@@ -21,13 +21,16 @@ use warnings;
use GD::Graph::bars;
use Data::Dumper;
use PerlIO::gzip;
+use File::Basename;
if (scalar @ARGV==0) {
+ my $name = basename($0);
+
print<<END;
Create a Linker Clipping Information Histogram
-usage: $0 INPUT_FILE.FA OUTPUT_FILE.PNG
+usage: $name INPUT_FILE.FA OUTPUT_FILE.PNG
INPUT_FILE.FA = input file (in FASTA format, can be GZIPped)
OUTPUT_FILE.PNG = histogram image
--- fastx-toolkit-0.0.14.orig/scripts/fastx_barcode_splitter.pl
+++ fastx-toolkit-0.0.14/scripts/fastx_barcode_splitter.pl
@@ -22,6 +22,7 @@ use IO::Handle;
use Data::Dumper;
use Getopt::Long;
use Carp;
+use File::Basename;
##
## This program splits a FASTQ/FASTA file into several smaller files,
@@ -349,6 +350,8 @@ sub open_and_detect_input_format
sub usage()
{
+ my $name = basename($0);
+
print<<EOF;
Barcode Splitter, by Assaf Gordon (gordon\@cshl.edu), 11sep2008
@@ -358,7 +361,7 @@ FASTA/FASTQ data is read from STDIN (for
Output files will be writen to disk.
Summary will be printed to STDOUT.
-usage: $0 --bcfile FILE --prefix PREFIX [--suffix SUFFIX] [--bol|--eol]
+usage: $name --bcfile FILE --prefix PREFIX [--suffix SUFFIX] [--bol|--eol]
[--mismatches N] [--exact] [--partial N] [--help] [--quiet] [--debug]
Arguments:
@@ -388,7 +391,7 @@ Arguments:
Example (Assuming 's_2_100.txt' is a FASTQ file, 'mybarcodes.txt' is
the barcodes file):
- \$ cat s_2_100.txt | $0 --bcfile mybarcodes.txt --bol --mismatches 2 \\
+ \$ cat s_2_100.txt | $name --bcfile mybarcodes.txt --bol --mismatches 2 \\
--prefix /tmp/bla_ --suffix ".txt"
Barcode file format
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