[med-svn] r9777 - in trunk/packages/sift/trunk/debian: . patches
H. Soon Gweon
soonio-guest at alioth.debian.org
Fri Feb 24 13:49:46 UTC 2012
Author: soonio-guest
Date: 2012-02-24 13:49:46 +0000 (Fri, 24 Feb 2012)
New Revision: 9777
Modified:
trunk/packages/sift/trunk/debian/links
trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path
Log:
Modified debian/links and some perl paths to make SIFT_exome_nssnvs.pl function properly.
Modified: trunk/packages/sift/trunk/debian/links
===================================================================
--- trunk/packages/sift/trunk/debian/links 2012-02-24 13:45:02 UTC (rev 9776)
+++ trunk/packages/sift/trunk/debian/links 2012-02-24 13:49:46 UTC (rev 9777)
@@ -1,5 +1,8 @@
usr/lib/sift/bin/info_on_seqs usr/bin/info_on_seqs
usr/lib/sift/bin/SIFT_exome_nssnvs.pl usr/bin/SIFT_exome_nssnvs.pl
+usr/lib/sift/bin/sift_feed_to_chr_coords_batch.pl usr/bin/sift_feed_to_chr_coords_batch.pl
+usr/lib/sift/bin/snv_db_engine.pl usr/bin/snv_db_engine.pl
+usr/lib/sift/bin/map_coords_to_bin.pl usr/bin/map_coords_to_bin.pl
usr/lib/sift/bin/SIFT_for_submitting_fasta_seq.csh usr/bin/SIFT_for_submitting_fasta_seq.csh
usr/lib/sift/bin/SIFT_for_submitting_fasta_seq.csh usr/bin/sift_for_submitting_fasta_seq.csh
usr/share/man/man1/SIFT_for_submitting_fasta_seq.csh.1.gz usr/share/man/man1/sift_for_submitting_fasta_seq.csh.1.gz
Modified: trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path
===================================================================
--- trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path 2012-02-24 13:45:02 UTC (rev 9776)
+++ trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path 2012-02-24 13:49:46 UTC (rev 9777)
@@ -3,10 +3,8 @@
* Enhance verbosity in csh scripts for bug hunting.
* Add blast processors argument SIFT_for_submitting_fasta_seq.csh .
* Trailing whitespace removed from lines.
-Index: sift-4.0.3b/bin/SIFT_exome_nssnvs.pl
-===================================================================
---- sift-4.0.3b.orig/bin/SIFT_exome_nssnvs.pl 2010-03-08 19:08:59.000000000 +0100
-+++ sift-4.0.3b/bin/SIFT_exome_nssnvs.pl 2012-02-23 18:57:19.447044528 +0100
+--- a/bin/SIFT_exome_nssnvs.pl
++++ b/bin/SIFT_exome_nssnvs.pl
@@ -1,4 +1,8 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -35,10 +33,8 @@
my $Variation_db_dir = $opt_d;
mkdir $tmp;
my $num_coords_per_split = 1000;
-Index: sift-4.0.3b/bin/SIFT_exome_indels.pl
-===================================================================
---- sift-4.0.3b.orig/bin/SIFT_exome_indels.pl 2010-03-08 19:00:00.000000000 +0100
-+++ sift-4.0.3b/bin/SIFT_exome_indels.pl 2012-02-23 18:57:19.451044490 +0100
+--- a/bin/SIFT_exome_indels.pl
++++ b/bin/SIFT_exome_indels.pl
@@ -1,4 +1,6 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -65,20 +61,16 @@
require "$bin/SIFT_subroutines.pm";
mkdir $tmp;
chmod 0777, $tmp;
-Index: sift-4.0.3b/bin/perlscripts/get_BLINK_seq.pl
-===================================================================
---- sift-4.0.3b.orig/bin/perlscripts/get_BLINK_seq.pl 2010-03-08 18:59:21.000000000 +0100
-+++ sift-4.0.3b/bin/perlscripts/get_BLINK_seq.pl 2012-02-23 18:57:19.467044434 +0100
+--- a/bin/perlscripts/get_BLINK_seq.pl
++++ b/bin/perlscripts/get_BLINK_seq.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
#use strict;
use LWP::Simple;
use LWP::UserAgent;
-Index: sift-4.0.3b/bin/seqs_chosen_via_median_info.csh
-===================================================================
---- sift-4.0.3b.orig/bin/seqs_chosen_via_median_info.csh 2010-03-08 19:00:42.000000000 +0100
-+++ sift-4.0.3b/bin/seqs_chosen_via_median_info.csh 2012-02-23 18:57:19.475044542 +0100
+--- a/bin/seqs_chosen_via_median_info.csh
++++ b/bin/seqs_chosen_via_median_info.csh
@@ -1,7 +1,8 @@
-#!/bin/csh
+#!/bin/csh -e
@@ -231,10 +223,8 @@
exit (0)
-
-
-Index: sift-4.0.3b/bin/SIFT_for_submitting_fasta_seq.csh
-===================================================================
---- sift-4.0.3b.orig/bin/SIFT_for_submitting_fasta_seq.csh 2010-03-08 19:09:47.000000000 +0100
-+++ sift-4.0.3b/bin/SIFT_for_submitting_fasta_seq.csh 2012-02-23 18:57:19.483044535 +0100
+--- a/bin/SIFT_for_submitting_fasta_seq.csh
++++ b/bin/SIFT_for_submitting_fasta_seq.csh
@@ -1,4 +1,4 @@
-#!/bin/csh
+#!/bin/csh -e
@@ -292,10 +282,8 @@
+echo "Output in ($PWD/)$tmpsift"
exit
-Index: sift-4.0.3b/bin/SIFT_for_submitting_NCBI_gi_id.csh
-===================================================================
---- sift-4.0.3b.orig/bin/SIFT_for_submitting_NCBI_gi_id.csh 2010-03-08 19:08:31.000000000 +0100
-+++ sift-4.0.3b/bin/SIFT_for_submitting_NCBI_gi_id.csh 2012-02-23 18:57:19.487044671 +0100
+--- a/bin/SIFT_for_submitting_NCBI_gi_id.csh
++++ b/bin/SIFT_for_submitting_NCBI_gi_id.csh
@@ -1,4 +1,4 @@
-#!/bin/csh
+#!/bin/csh -e
@@ -382,10 +370,8 @@
exit
-Index: sift-4.0.3b/src/Alignment.c
-===================================================================
---- sift-4.0.3b.orig/src/Alignment.c 2009-11-23 19:13:34.000000000 +0100
-+++ sift-4.0.3b/src/Alignment.c 2012-02-23 18:57:19.499044525 +0100
+--- a/src/Alignment.c
++++ b/src/Alignment.c
@@ -17,7 +17,7 @@
#define _ALIGNMENT_C_
#include "PN_convert.c"
@@ -490,10 +476,8 @@
return no_of_clumps;
} /* end of cluster */
-Index: sift-4.0.3b/src/blocklist.c
-===================================================================
---- sift-4.0.3b.orig/src/blocklist.c 2009-11-23 19:13:34.000000000 +0100
-+++ sift-4.0.3b/src/blocklist.c 2012-02-23 18:57:19.507044729 +0100
+--- a/src/blocklist.c
++++ b/src/blocklist.c
@@ -9,7 +9,7 @@
#include <string.h>
#include "blocklist.h"
@@ -503,10 +487,8 @@
/*======================================================================
routines for a list of blocks
-Index: sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c
-===================================================================
---- sift-4.0.3b.orig/src/choose_seqs_via_psiblastseedmedian.c 2009-11-23 19:13:34.000000000 +0100
-+++ sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c 2012-02-23 18:57:19.515044579 +0100
+--- a/src/choose_seqs_via_psiblastseedmedian.c
++++ b/src/choose_seqs_via_psiblastseedmedian.c
@@ -1,6 +1,6 @@
/* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
@@ -864,10 +846,8 @@
{
FILE* fp;
-Index: sift-4.0.3b/src/clump_output_alignedseq.c
-===================================================================
---- sift-4.0.3b.orig/src/clump_output_alignedseq.c 2009-11-23 19:13:34.000000000 +0100
-+++ sift-4.0.3b/src/clump_output_alignedseq.c 2012-02-23 18:57:19.519044624 +0100
+--- a/src/clump_output_alignedseq.c
++++ b/src/clump_output_alignedseq.c
@@ -25,7 +25,7 @@
#include "Clumping.c"
@@ -895,10 +875,8 @@
}
-Index: sift-4.0.3b/src/consensus_to_seq.c
-===================================================================
---- sift-4.0.3b.orig/src/consensus_to_seq.c 2009-11-23 19:13:34.000000000 +0100
-+++ sift-4.0.3b/src/consensus_to_seq.c 2012-02-23 18:57:19.527044570 +0100
+--- a/src/consensus_to_seq.c
++++ b/src/consensus_to_seq.c
@@ -120,7 +120,7 @@
else
{
@@ -926,10 +904,8 @@
}
if ( (*outfp = fopen (outfilename, "w")) == NULL)
{
-Index: sift-4.0.3b/src/info_on_seqs.c
-===================================================================
---- sift-4.0.3b.orig/src/info_on_seqs.c 2009-11-23 19:13:34.000000000 +0100
-+++ sift-4.0.3b/src/info_on_seqs.c 2012-02-23 18:57:19.531044519 +0100
+--- a/src/info_on_seqs.c
++++ b/src/info_on_seqs.c
@@ -11,7 +11,7 @@
#include "Psiblast.c"
/* #include "Information.c */
@@ -1015,10 +991,8 @@
}
strcpy (errorfilename, outfilename);
-Index: sift-4.0.3b/src/Makefile
-===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ sift-4.0.3b/src/Makefile 2012-02-23 18:57:19.535044487 +0100
+--- /dev/null
++++ b/src/Makefile
@@ -0,0 +1,42 @@
+include-prefix := $(prefix)
+lib-prefix := $(prefix)
@@ -1062,10 +1036,8 @@
+include deps.mk
+
+# vim:ai:
-Index: sift-4.0.3b/src/Matrix_Info.c
-===================================================================
---- sift-4.0.3b.orig/src/Matrix_Info.c 2009-11-23 19:13:33.000000000 +0100
-+++ sift-4.0.3b/src/Matrix_Info.c 2012-02-23 18:57:19.550918309 +0100
+--- a/src/Matrix_Info.c
++++ b/src/Matrix_Info.c
@@ -384,7 +384,7 @@
int pos_observed_tolerant, pos_error_tn, pos_notobserved_intolerant,
pos_error_fp, pos_total;
@@ -1199,10 +1171,8 @@
while (fgets (line, LARGE_BUFF_LENGTH, infofp) != NULL) {
word1[0] = '\0'; word2[0] = '\0';
stringp = strtok (line, " \r\n\t");
-Index: sift-4.0.3b/src/PN_blocks.c
-===================================================================
---- sift-4.0.3b.orig/src/PN_blocks.c 2009-11-23 19:13:34.000000000 +0100
-+++ sift-4.0.3b/src/PN_blocks.c 2012-02-23 18:57:19.558918350 +0100
+--- a/src/PN_blocks.c
++++ b/src/PN_blocks.c
@@ -671,7 +671,7 @@
Block* newblock;
Residue* residue_pointer;
@@ -1212,10 +1182,8 @@
non_X_length = 0;
for (i=0; i < block->width; i++) {
-Index: sift-4.0.3b/src/PN_convert.c
-===================================================================
---- sift-4.0.3b.orig/src/PN_convert.c 2009-11-23 19:13:34.000000000 +0100
-+++ sift-4.0.3b/src/PN_convert.c 2012-02-23 18:57:19.566886394 +0100
+--- a/src/PN_convert.c
++++ b/src/PN_convert.c
@@ -1,6 +1,6 @@
/* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
@@ -2271,10 +2239,8 @@
}
-Index: sift-4.0.3b/src/Protdist.c
-===================================================================
---- sift-4.0.3b.orig/src/Protdist.c 2009-11-23 19:13:34.000000000 +0100
-+++ sift-4.0.3b/src/Protdist.c 2012-02-23 18:57:19.575044563 +0100
+--- a/src/Protdist.c
++++ b/src/Protdist.c
@@ -124,7 +124,7 @@
{
double max_dist;
@@ -2284,10 +2250,8 @@
max_dist = 0;
-Index: sift-4.0.3b/src/Psiblast.c
-===================================================================
---- sift-4.0.3b.orig/src/Psiblast.c 2009-11-23 19:13:33.000000000 +0100
-+++ sift-4.0.3b/src/Psiblast.c 2012-02-23 18:57:19.586919315 +0100
+--- a/src/Psiblast.c
++++ b/src/Psiblast.c
@@ -1,6 +1,6 @@
/* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
@@ -2489,10 +2453,8 @@
} /* end get_top_seq */
#endif
-Index: sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c
-===================================================================
---- sift-4.0.3b.orig/src/psiblast_res_to_fasta_dbpairwise.c 2009-11-23 19:13:33.000000000 +0100
-+++ sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c 2012-02-23 18:57:19.647044663 +0100
+--- a/src/psiblast_res_to_fasta_dbpairwise.c
++++ b/src/psiblast_res_to_fasta_dbpairwise.c
@@ -32,8 +32,8 @@
#include "Protdist.c"
#include "Psiblast.c"
@@ -2578,10 +2540,8 @@
fprintf (errorfp, "couldn't open %s in processing PSIBLAST results\n", filename);
exit (-1);
}
-Index: sift-4.0.3b/src/seqs_from_psiblast_res.c
-===================================================================
---- sift-4.0.3b.orig/src/seqs_from_psiblast_res.c 2009-11-23 19:13:33.000000000 +0100
-+++ sift-4.0.3b/src/seqs_from_psiblast_res.c 2012-02-23 18:57:19.651044467 +0100
+--- a/src/seqs_from_psiblast_res.c
++++ b/src/seqs_from_psiblast_res.c
@@ -23,7 +23,7 @@
#include "stringhash.c"
#include "Psiblast.c"
@@ -2615,10 +2575,8 @@
}
if ((*seqfp = fopen (seqfilename, "r")) == NULL)
-Index: sift-4.0.3b/src/sift_blimps.h
-===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ sift-4.0.3b/src/sift_blimps.h 2012-02-23 18:57:19.659044510 +0100
+--- /dev/null
++++ b/src/sift_blimps.h
@@ -0,0 +1,12 @@
+#ifndef SIFT_BLIMPS_H
+#define SIFT_BLIMPS_H
@@ -2632,10 +2590,8 @@
+}
+
+#endif
-Index: sift-4.0.3b/src/SortList.c
-===================================================================
---- sift-4.0.3b.orig/src/SortList.c 2009-11-23 19:13:33.000000000 +0100
-+++ sift-4.0.3b/src/SortList.c 2012-02-23 18:57:19.666926854 +0100
+--- a/src/SortList.c
++++ b/src/SortList.c
@@ -13,7 +13,7 @@
lowest_scoring_aa (Matrix* matrix, int pos)
{
@@ -2645,10 +2601,8 @@
double min;
min = 10000;
-Index: sift-4.0.3b/SIFT_for_submitting_fasta_seq.csh.pod
-===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ sift-4.0.3b/SIFT_for_submitting_fasta_seq.csh.pod 2012-02-23 18:57:19.675044442 +0100
+--- /dev/null
++++ b/SIFT_for_submitting_fasta_seq.csh.pod
@@ -0,0 +1,55 @@
+=head1 NAME
+
@@ -2705,150 +2659,130 @@
+=head1 SEE ALSO
+
+L<info_on_seqs>
-Index: sift-4.0.3b/bin/Classify_SNPs_Indels.pl
-===================================================================
---- sift-4.0.3b.orig/bin/Classify_SNPs_Indels.pl 2010-03-08 18:54:49.000000000 +0100
-+++ sift-4.0.3b/bin/Classify_SNPs_Indels.pl 2012-02-23 18:57:19.687004191 +0100
+--- a/bin/Classify_SNPs_Indels.pl
++++ b/bin/Classify_SNPs_Indels.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
$SIFT_HOME = $ENV{'SIFT_HOME'};
$bin = "$SIFT_HOME/bin";
-Index: sift-4.0.3b/bin/SIFT_intersect_cds.pl
-===================================================================
---- sift-4.0.3b.orig/bin/SIFT_intersect_cds.pl 2010-03-08 19:10:08.000000000 +0100
-+++ sift-4.0.3b/bin/SIFT_intersect_cds.pl 2012-02-23 18:57:19.695044575 +0100
+--- a/bin/SIFT_intersect_cds.pl
++++ b/bin/SIFT_intersect_cds.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
$| = 1;
use Getopt::Std;
use File::Basename;
-Index: sift-4.0.3b/bin/SNPClassifier/Classify_SNPs.pl
-===================================================================
---- sift-4.0.3b.orig/bin/SNPClassifier/Classify_SNPs.pl 2009-11-23 19:13:30.000000000 +0100
-+++ sift-4.0.3b/bin/SNPClassifier/Classify_SNPs.pl 2012-02-23 18:57:19.703044603 +0100
+--- a/bin/SNPClassifier/Classify_SNPs.pl
++++ b/bin/SNPClassifier/Classify_SNPs.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
###############################################################################
# #
-Index: sift-4.0.3b/bin/SNPClassifier/Extract_Coding_Info.pl
-===================================================================
---- sift-4.0.3b.orig/bin/SNPClassifier/Extract_Coding_Info.pl 2009-11-23 19:13:30.000000000 +0100
-+++ sift-4.0.3b/bin/SNPClassifier/Extract_Coding_Info.pl 2012-02-23 18:57:19.711041186 +0100
+--- a/bin/SNPClassifier/Extract_Coding_Info.pl
++++ b/bin/SNPClassifier/Extract_Coding_Info.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
###############################################################################
# #
-Index: sift-4.0.3b/bin/detect_indel.pl
-===================================================================
---- sift-4.0.3b.orig/bin/detect_indel.pl 2010-03-08 19:08:09.000000000 +0100
-+++ sift-4.0.3b/bin/detect_indel.pl 2012-02-23 18:57:19.715044412 +0100
+--- a/bin/detect_indel.pl
++++ b/bin/detect_indel.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
# This program is licensed to you under the Fred
-Index: sift-4.0.3b/bin/detect_repeat.pl
-===================================================================
---- sift-4.0.3b.orig/bin/detect_repeat.pl 2010-03-08 19:12:09.000000000 +0100
-+++ sift-4.0.3b/bin/detect_repeat.pl 2012-02-23 18:57:19.723044449 +0100
+--- a/bin/detect_repeat.pl
++++ b/bin/detect_repeat.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# This program is licensed to you under the Fred
# Hutchinos Cancer Research Center (FHCRC)
-Index: sift-4.0.3b/bin/get_sequences.pl
-===================================================================
---- sift-4.0.3b.orig/bin/get_sequences.pl 2010-03-08 18:57:38.000000000 +0100
-+++ sift-4.0.3b/bin/get_sequences.pl 2012-02-23 18:57:19.727044469 +0100
+--- a/bin/get_sequences.pl
++++ b/bin/get_sequences.pl
@@ -1,4 +1,4 @@
-#! /opt/local/bin/perl5 -w
+#!/usr/bin/perl -w
#####################################################################
#
-Index: sift-4.0.3b/bin/indelfile_to_gff.pl
-===================================================================
---- sift-4.0.3b.orig/bin/indelfile_to_gff.pl 2010-03-08 19:12:29.000000000 +0100
-+++ sift-4.0.3b/bin/indelfile_to_gff.pl 2012-02-23 18:57:19.731044505 +0100
+--- a/bin/indelfile_to_gff.pl
++++ b/bin/indelfile_to_gff.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# This program is licensed to you under the Fred
# Hutchinos Cancer Research Center (FHCRC)
# NONCOMMERICAL LICENSE. A copy of the license may be found at
-Index: sift-4.0.3b/bin/map_coords_to_bin.pl
-===================================================================
---- sift-4.0.3b.orig/bin/map_coords_to_bin.pl 2010-03-08 19:12:47.000000000 +0100
-+++ sift-4.0.3b/bin/map_coords_to_bin.pl 2012-02-23 18:57:19.739044482 +0100
+--- a/bin/map_coords_to_bin.pl
++++ b/bin/map_coords_to_bin.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# This program is licensed to you under the Fred
# Hutchinos Cancer Research Center (FHCRC)
-Index: sift-4.0.3b/bin/map_coords_to_bin_indels.pl
-===================================================================
---- sift-4.0.3b.orig/bin/map_coords_to_bin_indels.pl 2010-03-08 19:13:11.000000000 +0100
-+++ sift-4.0.3b/bin/map_coords_to_bin_indels.pl 2012-02-23 18:57:19.747044533 +0100
+--- a/bin/map_coords_to_bin_indels.pl
++++ b/bin/map_coords_to_bin_indels.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# This program is licensed to you under the Fred
-Index: sift-4.0.3b/bin/model_transcript.pl
-===================================================================
---- sift-4.0.3b.orig/bin/model_transcript.pl 2010-03-08 19:12:57.000000000 +0100
-+++ sift-4.0.3b/bin/model_transcript.pl 2012-02-23 18:57:19.751044465 +0100
+--- a/bin/model_transcript.pl
++++ b/bin/model_transcript.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use DBI;
my $SIFT_HOME = $ENV{'SIFT_HOME'};
-Index: sift-4.0.3b/bin/reformat_chrfile.pl
-===================================================================
---- sift-4.0.3b.orig/bin/reformat_chrfile.pl 2010-03-08 19:00:22.000000000 +0100
-+++ sift-4.0.3b/bin/reformat_chrfile.pl 2012-02-23 18:57:19.755044452 +0100
+--- a/bin/reformat_chrfile.pl
++++ b/bin/reformat_chrfile.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# This program is licensed to you under the Fred
# Hutchinos Cancer Research Center (FHCRC)
-Index: sift-4.0.3b/bin/sift_feed_to_chr_coords_batch.pl
-===================================================================
---- sift-4.0.3b.orig/bin/sift_feed_to_chr_coords_batch.pl 2010-03-08 19:00:53.000000000 +0100
-+++ sift-4.0.3b/bin/sift_feed_to_chr_coords_batch.pl 2012-02-23 18:57:19.763044525 +0100
+--- a/bin/sift_feed_to_chr_coords_batch.pl
++++ b/bin/sift_feed_to_chr_coords_batch.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
my $SIFT_HOME = $ENV{'SIFT_HOME'};
my $bin = "$SIFT_HOME/bin";
-Index: sift-4.0.3b/bin/snv_db_engine.pl
-===================================================================
---- sift-4.0.3b.orig/bin/snv_db_engine.pl 2010-02-20 02:32:17.000000000 +0100
-+++ sift-4.0.3b/bin/snv_db_engine.pl 2012-02-23 18:57:19.771044564 +0100
+--- a/bin/snv_db_engine.pl
++++ b/bin/snv_db_engine.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
use Class::Struct;
#
-Index: sift-4.0.3b/src/Clumping.c
-===================================================================
---- sift-4.0.3b.orig/src/Clumping.c 2009-11-23 19:13:34.000000000 +0100
-+++ sift-4.0.3b/src/Clumping.c 2012-02-23 18:57:19.779044548 +0100
+@@ -17,7 +17,8 @@
+ system("umask 006");
+ my $bin = "$SIFT_HOME/bin";
+ $snp_classifier = "$bin/Classify_SNPs.pl";
+-require 'SIFT_subroutines.pm';
++use lib '/usr/lib/sift/bin';
++use SIFT_subroutines;
+ my $tmp = $ARGV[0];
+ my $Variation_db_dir = $ARGV[1];
+ my $master_pid = $ARGV[2];
+--- a/src/Clumping.c
++++ b/src/Clumping.c
@@ -183,7 +183,7 @@
printf ("Clumped %d sequences into %d clusters\n", nseq, iclus);
/* keep this print because get # of clustersin awk statement */
@@ -2867,10 +2801,8 @@
return no_of_clumps;
} /* end of cluster */
-Index: sift-4.0.3b/info_on_seqs.pod
-===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ sift-4.0.3b/info_on_seqs.pod 2012-02-23 19:04:55.246919579 +0100
+--- /dev/null
++++ b/info_on_seqs.pod
@@ -0,0 +1,46 @@
+=head1 NAME
+
More information about the debian-med-commit
mailing list