[med-svn] [prodigal] 01/06: Imported Upstream version 2.6.3
Andreas Tille
tille at debian.org
Sat Feb 20 10:55:50 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository prodigal.
commit ea2b215e11ca5d2da03d46168d1d809e520f79be
Author: Andreas Tille <tille at debian.org>
Date: Sat Feb 20 07:49:12 2016 +0100
Imported Upstream version 2.6.3
---
CHANGES | 5 +++++
Makefile | 6 +++---
README.md | 7 +++----
VERSION | 2 +-
bitmap.c | 2 +-
bitmap.h | 2 +-
dprog.c | 2 +-
dprog.h | 2 +-
gene.c | 6 +++---
gene.h | 2 +-
main.c | 6 +++---
metagenomic.c | 2 +-
metagenomic.h | 2 +-
node.c | 2 +-
node.h | 2 +-
sequence.c | 2 +-
sequence.h | 2 +-
training.c | 2 +-
training.h | 2 +-
19 files changed, 31 insertions(+), 27 deletions(-)
diff --git a/CHANGES b/CHANGES
index 71da30e..9caeccb 100644
--- a/CHANGES
+++ b/CHANGES
@@ -1,3 +1,8 @@
+VERSION 2.6.3
+
+* Fixed a bug in protein translation output of partial genes where TTG/GTG
+codons were being incorrectly translated to methionine.
+
VERSION 2.6.2
* Added support for translation table 25.
diff --git a/Makefile b/Makefile
index c521391..23ffe00 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
##############################################################################
# PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
-# Copyright (C) 2007-2014 University of Tennessee / UT-Battelle
+# Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
#
# Code Author: Doug Hyatt
#
@@ -21,8 +21,8 @@
SHELL = /bin/sh
CC = gcc
-CFLAGS = -pedantic -Wall -O3
-LFLAGS = -lm
+CFLAGS += -pedantic -Wall -O3
+LFLAGS = -lm $(LDFLAGS)
TARGET = prodigal
SOURCES = $(shell echo *.c)
diff --git a/README.md b/README.md
index 961216d..590505b 100644
--- a/README.md
+++ b/README.md
@@ -8,10 +8,9 @@ prodigal -i my.metagenome.fna -o my.genes -a my.proteins.faa -p meta
prodigal -h
```
-### New in 2.6.2
- * Added support for translation table 25.
- * Fixed another bug affecting the Mac version.
- * Fixed an error in the 'uninstall' portion of the Makefile.
+### New in 2.6.3 (February 2016)
+ * Fixed a bug in protein translation output of partial genes where TTG/GTG
+codons were being incorrectly translated to methionine.
### Getting Started
diff --git a/VERSION b/VERSION
index d83a1f4..0a93b13 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-v2.6.2: February 2015
+v2.6.3: February 2016
diff --git a/bitmap.c b/bitmap.c
index ece5d50..64ae23b 100644
--- a/bitmap.c
+++ b/bitmap.c
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
diff --git a/bitmap.h b/bitmap.h
index 0b8aa69..dc3002c 100644
--- a/bitmap.h
+++ b/bitmap.h
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
diff --git a/dprog.c b/dprog.c
index 5568267..e30598a 100644
--- a/dprog.c
+++ b/dprog.c
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
diff --git a/dprog.h b/dprog.h
index a4d9388..d729f4c 100644
--- a/dprog.h
+++ b/dprog.h
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
diff --git a/gene.c b/gene.c
index bbcb2c9..ebaf2e8 100644
--- a/gene.c
+++ b/gene.c
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
@@ -445,7 +445,7 @@ void write_translations(FILE *fh, struct _gene *genes, int ng, struct
for(j = genes[i].begin; j < genes[i].end; j+=3) {
if(is_n(useq, j-1) == 1 || is_n(useq, j) == 1 || is_n(useq, j+1) == 1)
fprintf(fh, "X");
- else fprintf(fh, "%c", amino(seq, j-1, tinf, j==genes[i].begin?1:0 &&
+ else fprintf(fh, "%c", amino(seq, j-1, tinf, (j==genes[i].begin?1:0) &&
(1-nod[genes[i].start_ndx].edge)));
if((j-genes[i].begin)%180 == 177) fprintf(fh, "\n");
}
@@ -458,7 +458,7 @@ void write_translations(FILE *fh, struct _gene *genes, int ng, struct
if(is_n(useq, slen-j) == 1 || is_n(useq, slen-1-j) == 1 ||
is_n(useq, slen-2-j) == 1)
fprintf(fh, "X");
- else fprintf(fh, "%c", amino(rseq, j-1, tinf, j==slen+1-genes[i].end?1:0
+ else fprintf(fh, "%c", amino(rseq, j-1, tinf, (j==slen+1-genes[i].end?1:0)
&& (1-nod[genes[i].start_ndx].edge)));
if((j-slen-1+genes[i].end)%180 == 177) fprintf(fh, "\n");
}
diff --git a/gene.h b/gene.h
index 83f254c..a96a067 100644
--- a/gene.h
+++ b/gene.h
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
diff --git a/main.c b/main.c
index 00726b7..8893590 100644
--- a/main.c
+++ b/main.c
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
@@ -26,8 +26,8 @@
#include "dprog.h"
#include "gene.h"
-#define VERSION "2.6.2"
-#define DATE "February, 2015"
+#define VERSION "2.6.3"
+#define DATE "February, 2016"
#define MIN_SINGLE_GENOME 20000
#define IDEAL_SINGLE_GENOME 100000
diff --git a/metagenomic.c b/metagenomic.c
index 20a438a..2cb8bf9 100644
--- a/metagenomic.c
+++ b/metagenomic.c
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
diff --git a/metagenomic.h b/metagenomic.h
index 7ec6fcf..294ad3e 100644
--- a/metagenomic.h
+++ b/metagenomic.h
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
diff --git a/node.c b/node.c
index 2eba4e4..00f12ae 100644
--- a/node.c
+++ b/node.c
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
diff --git a/node.h b/node.h
index e694da4..6c722be 100644
--- a/node.h
+++ b/node.h
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
diff --git a/sequence.c b/sequence.c
index 76b318f..382fc38 100644
--- a/sequence.c
+++ b/sequence.c
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
diff --git a/sequence.h b/sequence.h
index c105860..c41adc4 100644
--- a/sequence.h
+++ b/sequence.h
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
diff --git a/training.c b/training.c
index 0bfc6bc..fa748da 100644
--- a/training.c
+++ b/training.c
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
diff --git a/training.h b/training.h
index 3044c87..2e4cbb0 100644
--- a/training.h
+++ b/training.h
@@ -1,6 +1,6 @@
/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
- Copyright (C) 2007-2015 University of Tennessee / UT-Battelle
+ Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
--
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