From 63ee98bbbbdea3b3e66ec88dbf9f9d88df53f9fe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=9Ckpepper=E2=80=9D?= <kp11@sanger.ac.uk>
Date: Fri, 2 Feb 2018 14:46:02 +0000
Subject: [PATCH] Minor script changes. Property name change
---
ChangeLog | 14 ++++++--
README.md | 9 ++++-
act | 34 +++++++++++++------
art | 34 +++++++++++++------
bamview | 31 +++++++++++------
dnaplotter | 31 ++++++++++++-----
.../artemis/components/alignment/BamView.java | 2 +-
7 files changed, 110 insertions(+), 45 deletions(-)
diff --git a/ChangeLog b/ChangeLog
index 68bded1cc..1682e03d5 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,4 +1,5 @@
Version 17
+
Artemis/ACT and associated applications have been upgraded to Java 8. Java 7/6/5 are now no longer supported - RT ticket #589103
BamView fixes/changes -
@@ -13,16 +14,18 @@ Version 17
9) Performance tweak for BAM file indexing.
10) Fixed issue in BamView whereby if you went to the end of a long contig and then switched to a shorter one (via the combo), you would end up off the end of the sequence
resulting in a negative array index exception. Code has been changed to reset display to the start of sequence when the combo is changed (i.e. same as Artemis).
+ 11) Added bamview_perform_detailed_validation boolean property that can be set to perform more detailed sam validation during loading - this can be slow for large files.
Added EvoSuite unit tests and additional targeted tests (RT ticket #419534: Develop a test suite for Artemis).
- Added Jacoco unit test coverage reporting - manual tests only currently. This may be switched to Clover in the future if this proves compatible with EvoSuite.
+ Added Jacoco unit test coverage reporting - manual tests only currently. This may be switched to Clover in the future if this proves compatible with EvoSuite
+ - for the moment we are stuck with two coverage reports - evosuite and Jacoco.
Removed redundant Corba libraries.
Upgraded JUnit jar.
- Changed Travis yml build file. RT ticket #597497: Set up artemis tests to run on travis.
+ Changed Travis yml build file. RT ticket #597497: Set up artemis tests to run on travis build.
Changed all build scripts and startup scripts - RT ticket #598617. Removed building of artemis_mac.jar which is not used.
Removed etc/gene_builder script and the gff2embl script (and documentation references) - no longer supported.
@@ -32,6 +35,13 @@ Version 17
Resized splash screen.
Added error handling for dnaplotter template file loading in standalone mode.
+
+ Added Bioconda recipe. RT ticket #341139 .
+
+ KNOWN ISSUES:
+ 1) Java JDKs 1.8.0_131 and above have a Swing bug related to overlaying of modal dialogs for Mac OS X: https://bugs.openjdk.java.net/browse/JDK-8179335
+ 2) There is a current bug in htsjdk whereby calls to the queryMate functionality can throw an exception on reads with secondaries and/or supplementals.
+ This affects looking up properties for a selected read on bamview - https://github.com/samtools/htsjdk/issues/1065
Version 16
Add 'Features Within Selection' option to the 'Select' menu to select
diff --git a/README.md b/README.md
index b82347002..8c175815d 100644
--- a/README.md
+++ b/README.md
@@ -21,7 +21,14 @@ The Artemis user manual is at:
http://www.sanger.ac.uk/science/tools/artemis
The ACT user manual is at:
- http://www.sanger.ac.uk/science/tools/act
+ http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act
+
+The DNA plotter user manual is at:
+ http://www.sanger.ac.uk/science/tools/dnaplotter
+
+The BAM View user manual is at:
+ http://www.sanger.ac.uk/science/tools/bamview
+
# INSTALLATION
diff --git a/act b/act
index 6f5789af6..f07e84da6 100755
--- a/act
+++ b/act
@@ -33,7 +33,7 @@ usage () {
echo " % act -Duserplot2=/pathToFile/userPlot"
echo
echo "HOMEPAGE"
- echo " http://www.sanger.ac.uk/resources/software/act/"
+ echo " http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act"
echo
exit 1
@@ -90,13 +90,8 @@ do
done
APPLICATION_HOME=`dirname "$PRG"`
-CLASSPATH=$APPLICATION_HOME:$APPLICATION_HOME/lib/biojava.jar:$APPLICATION_HOME/lib/jemAlign.jar:$APPLICATION_HOME/lib/jakarta-regexp-1.2.jar:$APPLICATION_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
-CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/batik/batik-awt-util.jar:$APPLICATION_HOME/lib/batik/batik-dom.jar:$APPLICATION_HOME/lib/batik/batik-ext.jar:$APPLICATION_HOME/lib/batik/batik-svggen.jar:$APPLICATION_HOME/lib/batik/batik-util.jar:$APPLICATION_HOME/lib/batik/batik-xml.jar:$APPLICATION_HOME/lib/batik/batik-codec.jar
-CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/j2ssh/commons-logging.jar:$APPLICATION_HOME/lib/j2ssh/j2ssh-core.jar:$APPLICATION_HOME/lib/j2ssh/
-CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$APPLICATION_HOME/lib/ibatis/:$APPLICATION_HOME/lib/ibatis/log4j-1.2.14.jar:$APPLICATION_HOME/lib/ibatis/cglib-nodep-2.2.jar
-CLASSPATH=$APPLICATION_HOME/lib/picard/picard.jar:$APPLICATION_HOME/lib/commons-net-3.6.jar:$CLASSPATH
-CLASSPATH=$APPLICATION_HOME/lib/commons-lang-2.6.jar:$CLASSPATH
-export CLASSPATH
+JAR_NAME=act.jar
+JAR_FILE=$APPLICATION_HOME/$JAR_NAME
#
# Use a custom Java version if necessary
@@ -120,7 +115,7 @@ add_proxy_properties
#
if [[ "$ARTEMIS_JVM_FLAGS" = "" ]]
then
- FLAGS="-mx1g -ms100m -noverify"
+ FLAGS="-mx2g -ms100m -noverify"
else
FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
fi
@@ -136,5 +131,22 @@ then
echo "Starting ACT with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi
-$JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.components.ActMain $*
-exit $?
+if [[ -e $JAR_FILE ]]
+then
+ $JAVA $FLAGS $APPLICATION_PROPERTIES -jar $JAR_FILE $*
+ result=$?
+else
+ CLASSPATH=$APPLICATION_HOME:$APPLICATION_HOME/lib/biojava.jar:$APPLICATION_HOME/lib/jemAlign.jar:$APPLICATION_HOME/lib/jakarta-regexp-1.2.jar:$APPLICATION_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
+ CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/batik/batik-awt-util.jar:$APPLICATION_HOME/lib/batik/batik-dom.jar:$APPLICATION_HOME/lib/batik/batik-ext.jar:$APPLICATION_HOME/lib/batik/batik-svggen.jar:$APPLICATION_HOME/lib/batik/batik-util.jar:$APPLICATION_HOME/lib/batik/batik-xml.jar:$APPLICATION_HOME/lib/batik/batik-codec.jar
+ CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/j2ssh/commons-logging.jar:$APPLICATION_HOME/lib/j2ssh/j2ssh-core.jar:$APPLICATION_HOME/lib/j2ssh/
+ CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$APPLICATION_HOME/lib/ibatis/:$APPLICATION_HOME/lib/ibatis/log4j-1.2.14.jar:$APPLICATION_HOME/lib/ibatis/cglib-nodep-2.2.jar
+ CLASSPATH=$APPLICATION_HOME/lib/picard/picard.jar:$APPLICATION_HOME/lib/commons-net-3.6.jar:$CLASSPATH
+ CLASSPATH=$APPLICATION_HOME/lib/commons-lang-2.6.jar:$CLASSPATH
+ export CLASSPATH
+
+ $JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.components.ActMain $*
+ result=$?
+fi
+
+exit $result
+
diff --git a/art b/art
index dd05bf054..ce30ace7b 100755
--- a/art
+++ b/art
@@ -39,7 +39,7 @@ usage () {
echo " % art -Dblack_belt_mode=true -Dbam=ecoli_hiseq.bam E_coli_K12.gbk"
echo " % art -Duserplot=repeatmap.plot,geecee.plot Plasmid.gff3"
echo "HOMEPAGE"
- echo " http://www.sanger.ac.uk/resources/software/artemis/"
+ echo " http://www.sanger.ac.uk/science/tools/artemis"
echo
exit 1
@@ -96,13 +96,8 @@ do
done
APPLICATION_HOME=`dirname "$PRG"`
-CLASSPATH=$APPLICATION_HOME:$APPLICATION_HOME/lib/biojava.jar:$APPLICATION_HOME/lib/jemAlign.jar:$APPLICATION_HOME/lib/jakarta-regexp-1.2.jar:$APPLICATION_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
-CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/batik/batik-awt-util.jar:$APPLICATION_HOME/lib/batik/batik-dom.jar:$APPLICATION_HOME/lib/batik/batik-ext.jar:$APPLICATION_HOME/lib/batik/batik-svggen.jar:$APPLICATION_HOME/lib/batik/batik-util.jar:$APPLICATION_HOME/lib/batik/batik-xml.jar:$APPLICATION_HOME/lib/batik/batik-codec.jar
-CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/j2ssh/commons-logging.jar:$APPLICATION_HOME/lib/j2ssh/j2ssh-core.jar:$APPLICATION_HOME/lib/j2ssh/
-CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$APPLICATION_HOME/lib/ibatis/:$APPLICATION_HOME/lib/ibatis/log4j-1.2.14.jar:$APPLICATION_HOME/lib/ibatis/cglib-nodep-2.2.jar
-CLASSPATH=$APPLICATION_HOME/lib/picard/picard.jar:$APPLICATION_HOME/lib/commons-net-3.6.jar:$CLASSPATH
-CLASSPATH=$APPLICATION_HOME/lib/commons-lang-2.6.jar:$CLASSPATH
-export CLASSPATH
+JAR_NAME=artemis.jar
+JAR_FILE=$APPLICATION_HOME/$JAR_NAME
#
# Use a custom Java version if necessary
@@ -126,7 +121,7 @@ add_proxy_properties
#
if [[ "$ARTEMIS_JVM_FLAGS" = "" ]]
then
- FLAGS="-mx1g -ms100m -noverify"
+ FLAGS="-mx2g -ms100m -noverify"
else
FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
fi
@@ -142,5 +137,22 @@ then
echo "Starting Artemis with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi
-$JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.components.ArtemisMain $*
-exit $?
+if [[ -e $JAR_FILE ]]
+then
+ $JAVA $FLAGS $APPLICATION_PROPERTIES -jar $JAR_FILE $*
+ result=$?
+else
+ CLASSPATH=$APPLICATION_HOME:$APPLICATION_HOME/lib/biojava.jar:$APPLICATION_HOME/lib/jemAlign.jar:$APPLICATION_HOME/lib/jakarta-regexp-1.2.jar:$APPLICATION_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
+ CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/batik/batik-awt-util.jar:$APPLICATION_HOME/lib/batik/batik-dom.jar:$APPLICATION_HOME/lib/batik/batik-ext.jar:$APPLICATION_HOME/lib/batik/batik-svggen.jar:$APPLICATION_HOME/lib/batik/batik-util.jar:$APPLICATION_HOME/lib/batik/batik-xml.jar:$APPLICATION_HOME/lib/batik/batik-codec.jar
+ CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/j2ssh/commons-logging.jar:$APPLICATION_HOME/lib/j2ssh/j2ssh-core.jar:$APPLICATION_HOME/lib/j2ssh/
+ CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$APPLICATION_HOME/lib/ibatis/:$APPLICATION_HOME/lib/ibatis/log4j-1.2.14.jar:$APPLICATION_HOME/lib/ibatis/cglib-nodep-2.2.jar
+ CLASSPATH=$APPLICATION_HOME/lib/picard/picard.jar:$APPLICATION_HOME/lib/commons-net-3.6.jar:$CLASSPATH
+ CLASSPATH=$APPLICATION_HOME/lib/commons-lang-2.6.jar:$CLASSPATH
+ export CLASSPATH
+
+ $JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.components.ArtemisMain $*
+ result=$?
+fi
+
+exit $result
+
diff --git a/bamview b/bamview
index 6515198fa..023300a5e 100755
--- a/bamview
+++ b/bamview
@@ -40,13 +40,8 @@ done
APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX $SANGER_ARTEMIS_OPTIONS"
APPLICATION_HOME=`dirname "$PRG"`
-CLASSPATH=$APPLICATION_HOME:$APPLICATION_HOME/lib/biojava.jar:$APPLICATION_HOME/lib/jemAlign.jar:$APPLICATION_HOME/lib/jakarta-regexp-1.2.jar:$APPLICATION_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
-CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/batik/batik-awt-util.jar:$APPLICATION_HOME/lib/batik/batik-dom.jar:$APPLICATION_HOME/lib/batik/batik-ext.jar:$APPLICATION_HOME/lib/batik/batik-svggen.jar:$APPLICATION_HOME/lib/batik/batik-util.jar:$APPLICATION_HOME/lib/batik/batik-xml.jar:$APPLICATION_HOME/lib/batik/batik-codec.jar
-CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/j2ssh/commons-logging.jar:$APPLICATION_HOME/lib/j2ssh/j2ssh-core.jar:$APPLICATION_HOME/lib/j2ssh/
-CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$APPLICATION_HOME/lib/ibatis/:$APPLICATION_HOME/lib/ibatis/log4j-1.2.14.jar:$APPLICATION_HOME/lib/ibatis/cglib-nodep-2.2.jar
-CLASSPATH=$APPLICATION_HOME/lib/picard/picard.jar:$APPLICATION_HOME/lib/commons-net-3.6.jar:$CLASSPATH
-CLASSPATH=$APPLICATION_HOME/lib/commons-lang-2.6.jar:$CLASSPATH
-export CLASSPATH
+JAR_NAME=bamview.jar
+JAR_FILE=$APPLICATION_HOME/$JAR_NAME
#
# Use a custom Java version if necessary
@@ -70,7 +65,7 @@ add_proxy_properties
#
if [[ "$ARTEMIS_JVM_FLAGS" = "" ]]
then
- FLAGS="-mx1g -ms100m -noverify"
+ FLAGS="-mx2g -ms100m -noverify"
else
FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
fi
@@ -86,5 +81,21 @@ then
echo "Starting BamView with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi
-$JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.components.alignment.BamView $*
-exit $?
+if [[ -e $JAR_FILE ]]
+then
+ $JAVA $FLAGS $APPLICATION_PROPERTIES -jar $JAR_FILE $*
+ result=$?
+else
+ CLASSPATH=$APPLICATION_HOME:$APPLICATION_HOME/lib/biojava.jar:$APPLICATION_HOME/lib/jemAlign.jar:$APPLICATION_HOME/lib/jakarta-regexp-1.2.jar:$APPLICATION_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
+ CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/batik/batik-awt-util.jar:$APPLICATION_HOME/lib/batik/batik-dom.jar:$APPLICATION_HOME/lib/batik/batik-ext.jar:$APPLICATION_HOME/lib/batik/batik-svggen.jar:$APPLICATION_HOME/lib/batik/batik-util.jar:$APPLICATION_HOME/lib/batik/batik-xml.jar:$APPLICATION_HOME/lib/batik/batik-codec.jar
+ CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/j2ssh/commons-logging.jar:$APPLICATION_HOME/lib/j2ssh/j2ssh-core.jar:$APPLICATION_HOME/lib/j2ssh/
+ CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$APPLICATION_HOME/lib/ibatis/:$APPLICATION_HOME/lib/ibatis/log4j-1.2.14.jar:$APPLICATION_HOME/lib/ibatis/cglib-nodep-2.2.jar
+ CLASSPATH=$APPLICATION_HOME/lib/picard/picard.jar:$APPLICATION_HOME/lib/commons-net-3.6.jar:$CLASSPATH
+ CLASSPATH=$APPLICATION_HOME/lib/commons-lang-2.6.jar:$CLASSPATH
+ export CLASSPATH
+
+ $JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.components.alignment.BamView $*
+ result=$?
+fi
+
+exit $result
diff --git a/dnaplotter b/dnaplotter
index b5ef64607..c3084d697 100755
--- a/dnaplotter
+++ b/dnaplotter
@@ -77,13 +77,8 @@ do
done
APPLICATION_HOME=`dirname "$PRG"`
-CLASSPATH=$APPLICATION_HOME:$APPLICATION_HOME/lib/biojava.jar:$APPLICATION_HOME/lib/jemAlign.jar:$APPLICATION_HOME/lib/jakarta-regexp-1.2.jar:$APPLICATION_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
-CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/j2ssh/commons-logging.jar:$APPLICATION_HOME/lib/j2ssh/j2ssh-core.jar:$APPLICATION_HOME/lib/j2ssh/
-CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$APPLICATION_HOME/lib/ibatis/:$APPLICATION_HOME/lib/ibatis/log4j-1.2.14.jar:$APPLICATION_HOME/lib/ibatis/cglib-nodep-2.2.jar
-CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/batik/batik-awt-util.jar:$APPLICATION_HOME/lib/batik/batik-dom.jar:$APPLICATION_HOME/lib/batik/batik-ext.jar:$APPLICATION_HOME/lib/batik/batik-svggen.jar:$APPLICATION_HOME/lib/batik/batik-util.jar:$APPLICATION_HOME/lib/batik/batik-xml.jar
-CLASSPATH=$APPLICATION_HOME/lib/picard/picard.jar:$APPLICATION_HOME/lib/commons-net-3.6.jar:$CLASSPATH
-CLASSPATH=$APPLICATION_HOME/lib/commons-lang-2.6.jar:$CLASSPATH
-export CLASSPATH
+JAR_NAME=dnaplotter.jar
+JAR_FILE=$APPLICATION_HOME/$JAR_NAME
#
# Use a custom Java version if necessary
@@ -107,7 +102,7 @@ add_proxy_properties
#
if [[ "$ARTEMIS_JVM_FLAGS" = "" ]]
then
- FLAGS="-mx1g -ms100m -noverify"
+ FLAGS="-mx2g -ms100m -noverify"
else
FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
fi
@@ -123,5 +118,23 @@ then
echo "Starting DNA Plotter with arguments: $FLAGS $APPLICATION_PROPERTIES $TEMPLATE_FILE_ARG"
fi
-$JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
+if [[ -e $JAR_FILE ]]
+then
+ $JAVA $FLAGS $APPLICATION_PROPERTIES -jar $JAR_FILE $TEMPLATE_FILE_ARG
+ result=$?
+else
+ CLASSPATH=$APPLICATION_HOME:$APPLICATION_HOME/lib/biojava.jar:$APPLICATION_HOME/lib/jemAlign.jar:$APPLICATION_HOME/lib/jakarta-regexp-1.2.jar:$APPLICATION_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
+ CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/j2ssh/commons-logging.jar:$APPLICATION_HOME/lib/j2ssh/j2ssh-core.jar:$APPLICATION_HOME/lib/j2ssh/
+ CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$APPLICATION_HOME/lib/ibatis/:$APPLICATION_HOME/lib/ibatis/log4j-1.2.14.jar:$APPLICATION_HOME/lib/ibatis/cglib-nodep-2.2.jar
+ CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/batik/batik-awt-util.jar:$APPLICATION_HOME/lib/batik/batik-dom.jar:$APPLICATION_HOME/lib/batik/batik-ext.jar:$APPLICATION_HOME/lib/batik/batik-svggen.jar:$APPLICATION_HOME/lib/batik/batik-util.jar:$APPLICATION_HOME/lib/batik/batik-xml.jar
+ CLASSPATH=$APPLICATION_HOME/lib/picard/picard.jar:$APPLICATION_HOME/lib/commons-net-3.6.jar:$CLASSPATH
+ CLASSPATH=$APPLICATION_HOME/lib/commons-lang-2.6.jar:$CLASSPATH
+ export CLASSPATH
+
+ $JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
+ result=$?
+fi
+
+exit $result
+
exit $?
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 132c1f4f4..5c4321ee2 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -346,7 +346,7 @@ public class BamView extends JPanel
}
}
- doInputFileValidation = Options.getOptions().getPropertyTruthValue("bamview_perform_file_validation");
+ doInputFileValidation = Options.getOptions().getPropertyTruthValue("bamview_perform_detailed_validation");
logger4j.debug("PERFORM UP-FRONT INPUT FILE VALIDATION=" + doInputFileValidation);
if(Options.getOptions().getIntegerProperty("bam_read_thread") != null)
--
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