0 | 0 |
Author: Kumar Appaiah
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1 | 1 |
Description: Fix #461691
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2 | 2 |
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--- glimmer3.02.orig/src/Common/delcher.cc
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+++ glimmer3.02/src/Common/delcher.cc
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--- a/src/Common/delcher.cc
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+++ b/src/Common/delcher.cc
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@@ -9,6 +9,7 @@
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#include "delcher.hh"
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const int COMMATIZE_BUFF_LEN = 50;
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// Length of buffer for creating string with commas
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--- glimmer3.02.orig/src/Common/fasta.cc
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+++ glimmer3.02/src/Common/fasta.cc
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--- a/src/Common/fasta.cc
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+++ b/src/Common/fasta.cc
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@@ -9,7 +9,7 @@
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#include "fasta.hh"
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void Fasta_Print
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(FILE * fp, const char * s, const char * hdr, int fasta_width)
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--- glimmer3.02.orig/src/Common/gene.cc
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+++ glimmer3.02/src/Common/gene.cc
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--- a/src/Common/gene.cc
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+++ b/src/Common/gene.cc
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@@ -10,6 +10,7 @@
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#include "delcher.hh"
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#include "gene.hh"
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static const char COMPLEMENT_TABLE []
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= "nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn"
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--- glimmer3.02.orig/src/Glimmer/anomaly.cc
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+++ glimmer3.02/src/Glimmer/anomaly.cc
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--- a/src/Glimmer/anomaly.cc
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+++ b/src/Glimmer/anomaly.cc
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@@ -12,6 +12,7 @@
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#include "anomaly.hh"
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// Global variables
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--- glimmer3.02.orig/src/ICM/icm.cc
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+++ glimmer3.02/src/ICM/icm.cc
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--- a/src/ICM/icm.cc
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+++ b/src/ICM/icm.cc
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@@ -15,6 +15,8 @@
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#include "icm.hh"
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using namespace std;
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extern int Verbose;
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--- glimmer3.02.orig/src/Util/entropy-score.cc
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+++ glimmer3.02/src/Util/entropy-score.cc
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--- a/src/Util/entropy-score.cc
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+++ b/src/Util/entropy-score.cc
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@@ -9,7 +9,7 @@
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// regions in it by entropy distance. Results are output
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// to stdout .
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#include "entropy-score.hh"
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--- glimmer3.02.orig/src/Glimmer/glimmer3.cc
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+++ glimmer3.02/src/Glimmer/glimmer3.cc
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--- a/src/Glimmer/glimmer3.cc
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+++ b/src/Glimmer/glimmer3.cc
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@@ -12,11 +12,10 @@
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// Copyright (c) 2006 University of Maryland Center for Bioinformatics
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// & Computational Biology
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static int For_Edwin = 0;
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--- glimmer3.02.orig/src/ICM/build-icm.cc
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+++ glimmer3.02/src/ICM/build-icm.cc
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--- a/src/ICM/build-icm.cc
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+++ b/src/ICM/build-icm.cc
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@@ -13,6 +13,7 @@
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#include "build-icm.hh"
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static int Genbank_Xlate_Code = 0;
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// Holds the Genbank translation table number that determines
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--- glimmer3.02.orig/src/Util/extract.cc
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+++ glimmer3.02/src/Util/extract.cc
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--- a/src/Util/extract.cc
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+++ b/src/Util/extract.cc
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@@ -9,7 +9,7 @@
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// sequences specified by coordinates. The resulting sequences
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// are output (in multifasta or two-string format) to stdout.
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#include "extract.hh"
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--- glimmer3.02.orig/src/Glimmer/glimmer2.cc
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+++ glimmer3.02/src/Glimmer/glimmer2.cc
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--- a/src/Glimmer/glimmer2.cc
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+++ b/src/Glimmer/glimmer2.cc
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@@ -37,6 +37,7 @@
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#include "delcher.h"
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#include "gene.h"
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const int DEFAULT_MIN_GENE_LEN = 90;
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const double DEFAULT_MIN_OLAP_PERCENT = 0.10;
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--- glimmer3.02.orig/src/Glimmer/long-orfs.cc
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+++ glimmer3.02/src/Glimmer/long-orfs.cc
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--- a/src/Glimmer/long-orfs.cc
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+++ b/src/Glimmer/long-orfs.cc
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@@ -15,7 +15,7 @@
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#include "long-orfs.hh"
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// External variables
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--- glimmer3.02.orig/src/ICM/build-fixed.cc
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+++ glimmer3.02/src/ICM/build-fixed.cc
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--- a/src/ICM/build-fixed.cc
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+++ b/src/ICM/build-fixed.cc
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@@ -12,6 +12,7 @@
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#include "build-fixed.hh"
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static FILE * Index_File_fp = NULL;
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// File containing a list of subscripts of strings to train model
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--- glimmer3.02.orig/src/ICM/score-fixed.cc
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+++ glimmer3.02/src/ICM/score-fixed.cc
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--- a/src/ICM/score-fixed.cc
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+++ b/src/ICM/score-fixed.cc
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@@ -8,6 +8,7 @@
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#include "score-fixed.hh"
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static char * Pos_Model_Path;
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// Name of file containing the positive model
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--- glimmer3.02.orig/src/Util/multi-extract.cc
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+++ glimmer3.02/src/Util/multi-extract.cc
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--- a/src/Util/multi-extract.cc
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+++ b/src/Util/multi-extract.cc
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@@ -10,7 +10,7 @@
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// resulting sequences are output (in multifasta or two-string format)
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// to stdout.
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#include "multi-extract.hh"
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--- glimmer3.02.orig/src/Util/start-codon-distrib.cc
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+++ glimmer3.02/src/Util/start-codon-distrib.cc
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--- a/src/Util/start-codon-distrib.cc
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+++ b/src/Util/start-codon-distrib.cc
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@@ -17,6 +17,7 @@
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#include "start-codon-distrib.hh"
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// External variables
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--- glimmer3.02.orig/src/Util/uncovered.cc
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+++ glimmer3.02/src/Util/uncovered.cc
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--- a/src/Util/uncovered.cc
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+++ b/src/Util/uncovered.cc
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@@ -10,7 +10,7 @@
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// specified in the file named as the second command-line argument.
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// Output is a multifasta file sent to stdout.
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