[med-svn] [tigr-glimmer] 02/07: New upstream version 3.02b
Andreas Tille
tille at debian.org
Tue Dec 13 10:27:24 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository tigr-glimmer.
commit eb1b8e541860a36112e86ecfa2d3540043766132
Author: Andreas Tille <tille at debian.org>
Date: Tue Dec 13 09:31:50 2016 +0100
New upstream version 3.02b
---
README | 23 +++++++++++++++++++++++
SimpleMake/delcher.hh | 2 +-
SimpleMake/gene.cc | 4 ++--
SimpleMake/glimmer3.cc | 20 ++++++++++++++++----
SimpleMake/icm.cc | 2 +-
src/Common/delcher.hh | 2 +-
src/Common/gene.cc | 4 ++--
src/Glimmer/glimmer3.cc | 20 ++++++++++++++++----
src/ICM/icm.cc | 2 +-
9 files changed, 63 insertions(+), 16 deletions(-)
diff --git a/README b/README
new file mode 100644
index 0000000..a55ed96
--- /dev/null
+++ b/README
@@ -0,0 +1,23 @@
+Full instructions for installing and running Glimmer are in file
+glim302notes.pdf in this directory.
+
+Here's a quick start guide for the inpatient:
+
+- To build all Glimmer programs, go to the src directory and type make
+ (or alternately gmake). This will create all the executable files
+ in the directory bin. Note that initially directories bin, lib and
+ obj are all empty.
+
+- Scripts for running the programs are in directory scripts. Each
+ needs to be edited near the top to specify the correct location
+ (give the full path) where you have the bin and scripts directories
+ on your system. Script g3-iterated.csh is generally the best to use
+ to make gene predictions from a single genome sequence without other
+ data.
+
+- Some scripts (including g3-iterated.csh) use the program elph, which
+ needs to be separately downloaded and installed. You can get it from
+ ccb.jhu.edu/software/ELPH/index.shtml
+
+- Help on options and command parameters for each program can be gotten
+ by running the program with a -h option.
diff --git a/SimpleMake/delcher.hh b/SimpleMake/delcher.hh
index 31a3834..5e19c7a 100644
--- a/SimpleMake/delcher.hh
+++ b/SimpleMake/delcher.hh
@@ -30,7 +30,7 @@
#include <iomanip>
#include <fstream>
#include <vector>
-#include <string>
+#include <cstring>
#include "exceptions.hh"
diff --git a/SimpleMake/gene.cc b/SimpleMake/gene.cc
index f1bc984..7ea164f 100644
--- a/SimpleMake/gene.cc
+++ b/SimpleMake/gene.cc
@@ -260,7 +260,7 @@ void PWM_t :: Print
// Print the contents of this PWM to fp .
{
- char * tag = "acgt";
+ const char * tag = "acgt";
int width;
int i, j;
@@ -443,7 +443,7 @@ int Char_Sub
// Return a subscript corresponding to character ch .
{
- char * p;
+ const char * p;
p = strchr (CONVERSION_STRING, tolower (ch));
if (p == NULL)
diff --git a/SimpleMake/glimmer3.cc b/SimpleMake/glimmer3.cc
index cbd0f4c..ff8a0c7 100644
--- a/SimpleMake/glimmer3.cc
+++ b/SimpleMake/glimmer3.cc
@@ -531,8 +531,14 @@ static void Disqualify
if (p == NULL)
return;
- for (q = p -> best_pred; q != NULL && cutoff <= q -> pos; q = q -> best_pred)
- q -> disqualified = true;
+ // Search to cutoff - Max_Olap_Bases to make sure we reach all nodes
+ // whose pos might be >= cutoff
+ for (q = p -> best_pred; q != NULL && cutoff - Max_Olap_Bases <= q -> pos;
+ q = q -> best_pred)
+ {
+ if (cutoff <= q -> pos)
+ q -> disqualified = true;
+ }
return;
}
@@ -2661,8 +2667,14 @@ static void Requalify
if (p == NULL)
return;
- for (q = p -> best_pred; q != NULL && cutoff <= q -> pos; q = q -> best_pred)
- q -> disqualified = false;
+ // Search to cutoff - Max_Olap_Bases to make sure we reach all nodes
+ // whose pos might be >= cutoff
+ for (q = p -> best_pred; q != NULL && cutoff - Max_Olap_Bases <= q -> pos;
+ q = q -> best_pred)
+ {
+ if (cutoff <= q -> pos)
+ q -> disqualified = false;
+ }
return;
}
diff --git a/SimpleMake/icm.cc b/SimpleMake/icm.cc
index d675c31..3376a75 100644
--- a/SimpleMake/icm.cc
+++ b/SimpleMake/icm.cc
@@ -1981,7 +1981,7 @@ int Subscript
// model) for character ch .
{
- char * p;
+ const char * p;
p = strchr (ALPHA_STRING, tolower (Filter (ch)));
if (p == NULL)
diff --git a/src/Common/delcher.hh b/src/Common/delcher.hh
index 31a3834..5e19c7a 100644
--- a/src/Common/delcher.hh
+++ b/src/Common/delcher.hh
@@ -30,7 +30,7 @@
#include <iomanip>
#include <fstream>
#include <vector>
-#include <string>
+#include <cstring>
#include "exceptions.hh"
diff --git a/src/Common/gene.cc b/src/Common/gene.cc
index f1bc984..7ea164f 100644
--- a/src/Common/gene.cc
+++ b/src/Common/gene.cc
@@ -260,7 +260,7 @@ void PWM_t :: Print
// Print the contents of this PWM to fp .
{
- char * tag = "acgt";
+ const char * tag = "acgt";
int width;
int i, j;
@@ -443,7 +443,7 @@ int Char_Sub
// Return a subscript corresponding to character ch .
{
- char * p;
+ const char * p;
p = strchr (CONVERSION_STRING, tolower (ch));
if (p == NULL)
diff --git a/src/Glimmer/glimmer3.cc b/src/Glimmer/glimmer3.cc
index cbd0f4c..ff8a0c7 100644
--- a/src/Glimmer/glimmer3.cc
+++ b/src/Glimmer/glimmer3.cc
@@ -531,8 +531,14 @@ static void Disqualify
if (p == NULL)
return;
- for (q = p -> best_pred; q != NULL && cutoff <= q -> pos; q = q -> best_pred)
- q -> disqualified = true;
+ // Search to cutoff - Max_Olap_Bases to make sure we reach all nodes
+ // whose pos might be >= cutoff
+ for (q = p -> best_pred; q != NULL && cutoff - Max_Olap_Bases <= q -> pos;
+ q = q -> best_pred)
+ {
+ if (cutoff <= q -> pos)
+ q -> disqualified = true;
+ }
return;
}
@@ -2661,8 +2667,14 @@ static void Requalify
if (p == NULL)
return;
- for (q = p -> best_pred; q != NULL && cutoff <= q -> pos; q = q -> best_pred)
- q -> disqualified = false;
+ // Search to cutoff - Max_Olap_Bases to make sure we reach all nodes
+ // whose pos might be >= cutoff
+ for (q = p -> best_pred; q != NULL && cutoff - Max_Olap_Bases <= q -> pos;
+ q = q -> best_pred)
+ {
+ if (cutoff <= q -> pos)
+ q -> disqualified = false;
+ }
return;
}
diff --git a/src/ICM/icm.cc b/src/ICM/icm.cc
index d675c31..3376a75 100644
--- a/src/ICM/icm.cc
+++ b/src/ICM/icm.cc
@@ -1981,7 +1981,7 @@ int Subscript
// model) for character ch .
{
- char * p;
+ const char * p;
p = strchr (ALPHA_STRING, tolower (Filter (ch)));
if (p == NULL)
--
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