diff --git a/ChangeLog b/ChangeLog
index e53acc570fef033730928dad5dc941d6ff1ebb78..1fdb233596c73a75ca6c0569ff09ffc6b545c8c9 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,4 +1,11 @@
-Version 17
+Version 17.0.2-test - TBD next release
+
+ 1) Added bamview_use_htsjdk_file_index_caching property to allow switching off of htsjdk caching for bam files.
+ This gets around a bug for large bams whereby parts of the bam fail to get loaded - RT ticket #624271.
+ See htsjdk GitHub issue 1127 for details.
+
+
+Version 17.0.1
Artemis/ACT and associated applications have been upgraded to Java 8. Java 7/6/5 are now no longer supported - RT ticket #589103
diff --git a/etc/log4j.properties b/etc/log4j.properties
index d3f56d1fb7964ea2c0e8ab0891ddb013dfe6a674..346d5096cf08cb7c5459965eb998e2ec3f9ad6aa 100644
--- a/etc/log4j.properties
+++ b/etc/log4j.properties
@@ -36,6 +36,7 @@ log4j.logger.uk.ac.sanger.artemis.components.genebuilder.cv.GoBox=DEBUG, R
log4j.logger.uk.ac.sanger.artemis.chado.ArtemisUtils=DEBUG, R
log4j.logger.uk.ac.sanger.artemis.components.database.DatabaseJPanel=DEBUG, R
log4j.logger.uk.ac.sanger.artemis.components.alignment.LookSeqPanel=DEBUG, R
+log4j.logger.uk.ac.sanger.artemis.components.alignment.BamView=INFO, R
log4j.logger.uk.ac.sanger.artemis.components.variant=DEBUG, R
log4j.logger.uk.ac.sanger.artemis.io.ReadAndWriteEntry=DEBUG, R
log4j.logger.uk.ac.sanger.artemis.io.GFFStreamFeature=DEBUG, R
diff --git a/etc/options b/etc/options
index f7879a0ede03d2492e81bc79f3b3268dc1ccc7e6..8e398bb1a77be73cfa52d348a18314bc661baf68 100644
--- a/etc/options
+++ b/etc/options
@@ -19,7 +19,6 @@
font_size = 12
-
# Set the name of the font to use in Artemis. These possibilites are
# available on all platforms:
# Dialog, DialogInput, Monospaced, Serif, SansSerif, Symbol.
@@ -47,7 +46,6 @@ genetic_code_default = 1
eukaryotic_start_codons = atg
prokaryotic_start_codons = atg gtg ttg
-
#
# Genetic Codes :
# http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
@@ -859,6 +857,8 @@ bam_read_thread = 2
# Max read coverage to display
bam_max_coverage = 1000000
bamview_ftp_buffer_size=10485760
+# The following setting is turned off due to htsjdk issue no. 1127 (see GitHub)
+bamview_use_htsjdk_file_index_caching=false
#
# CHADO DATABASE OPTIONS
diff --git a/etc/versions b/etc/versions
index 5bd9885cef78034c851e43ab9b58d181920de3ef..bc3133b5cbbc1ca6f46124ec7facb6686e2f6e82 100644
--- a/etc/versions
+++ b/etc/versions
@@ -1,4 +1,4 @@
-Artemis Release 17.0.1
-ACT Release 17.0.1
-DNAPlotter Release 17.0.1
-BamView 17.0.1
+Artemis Release 17.0.2-test
+ACT Release 17.0.2-test
+DNAPlotter Release 17.0.2-test
+BamView 17.0.2-test
diff --git a/lib/picard/VERSION.txt b/lib/picard/VERSION.txt
index 17e60c9edd3fbfa8de405c9aaa950b93b2b0d7c8..4e191748d114d4b1fb26eb2cd44bbcfc5c75be90 100644
--- a/lib/picard/VERSION.txt
+++ b/lib/picard/VERSION.txt
@@ -1,3 +1,4 @@
-Picard jar version - 2.17.2
+Picard jar version - 2.18.4
-This jar includes htsjdk and all dependency libraries.
+This jar includes the latest htsjdk and all dependency libraries.
+Downloaded from Github on 21/5/2018
diff --git a/lib/picard/picard.jar b/lib/picard/picard.jar
index 0a44ddb522fb5ca2b9d93e2b130ff28cf657dead..0c179bc5d4c653916d151c6c74c597f41de318c7 100644
Binary files a/lib/picard/picard.jar and b/lib/picard/picard.jar differ
diff --git a/test/build-test.xml b/test/build-test.xml
index 53fd27d60670457ef7753b8cc8c4b5dcc71c8584..39b3cf392dc5f92569f68035ea49d0037c17f775 100644
--- a/test/build-test.xml
+++ b/test/build-test.xml
@@ -357,6 +357,8 @@
<exclude name="**/chado/*"/>
<exclude name="**/*Database*"/>
<exclude name="**/DNADraw_ESTest.*"/>
+ <exclude name="**/ExternalApplication_ESTest.*"/>
+ <exclude name="**/PublicDBDocumentEntry_ESTest.*"/>
<!-- TODO The following excluded evosuite tests need fixing -->
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index edd48036e7a950caadc9a58be879a51cce8a66e9..c02a3d43c44463410994f32334d39b3d4a4ded09 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -276,6 +276,9 @@ public class BamView extends JPanel
/** Whether we should strictly validate upfront the input BAM/CRAM file.*/
boolean doInputFileValidation = false;
+ /** Whether to use htsjdk file index caching.*/
+ boolean useHtsjdkIndexCaching = false;
+
private volatile AtomicBoolean foundFatalErrors = new AtomicBoolean(false);
/** busy cursor */
@@ -365,7 +368,10 @@ public class BamView extends JPanel
{
logger4j.debug("BAM MAX COVERAGE="+Options.getOptions().getIntegerProperty("bam_max_coverage"));
MAX_COVERAGE = Options.getOptions().getIntegerProperty("bam_max_coverage");
- }
+ }
+
+ useHtsjdkIndexCaching = Options.getOptions().getPropertyTruthValue("bamview_use_htsjdk_file_index_caching");
+ logger4j.debug("USE HTSJDK BAM FILE INDEX CACHING=" + useHtsjdkIndexCaching);
try
{
@@ -524,7 +530,11 @@ public class BamView extends JPanel
// so need to set the default stringency (from properties).
//
final SamReaderFactory samReaderFactory = SamReaderFactory.makeDefault();
- samReaderFactory.enable(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES);
+ if (useHtsjdkIndexCaching)
+ samReaderFactory.enable(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES);
+ else
+ samReaderFactory.disable(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES);
+
samReaderFactory.disable(Option.EAGERLY_DECODE);
samReaderFactory.validationStringency(validationStringency);