Because this change could have impacts that we don't notice, I think it would be best for this change to sit on the development version (not release version) for another cycle. I think it should be released in IGB 9.0.2.

Some links...

Kiran's branch with the update:
https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1098-sam-so

Samtools java library documentation:
http://www.javadoc.io/doc/com.github.samtools/htsjdk/2.16.0

Google document summarizing testing process (share link):
https://docs.google.com/document/d/19_EYNgiJr-GJT5zSQ99ogrLw8_aO5rl2ejXiNUYwq9M/edit?usp=sharing

At this point, I have not found anything that makes me think we should not merge this into master.

There may be some lag in loading GFF3 files, but it is hard to say if this is much more pronounced in this branch than in master.
On mac it is a lag, on Windows (at least on one machine) GFF3 did not load; on another machine I think it did. GFF3 has already been targeted for this.

I think whatever issues we subsequently find can be addressed as their own issues. As a baseline, this looks like a good change.

Here is the google doc
https://docs.google.com/document/d/19_EYNgiJr-GJT5zSQ99ogrLw8_aO5rl2ejXiNUYwq9M/edit
(copy/pasted below, sorry the formatting turned nasty in the copy/paste process)

As part of issue IGBF-1098 Kiran had to update third party libraries.

Java file changed
File type affected in IGB
Test method
Test result
NibbleResiduesParser.java

SAMWriter.java

BNIB.java

Not worry about
NA
BaiZoomSymLoader.java

FastaIdx.java

GFF.java
.gff
Use smoke test quickload, load this file file type.
Look at images in File Formats to make sure it is displayed correctly.
Does this mean GTF? I can’t see any GFF file!
GFF3.java
.gff3
Use smoke test quickload, load this file file type.
Look at images in File Formats to make sure it is displayed correctly.
Does not load.
Did not load for a particular region too on Windows.

GFF3 from smoke testing QL does load on mac, but even a small region takes forever (about a full minute for chr1:61,009,789-61,561,938) takes a minute
IndexZoomSymLoader.java

LineProcessor.java

Doesn’t affect
Looks Good!
PSL.java

Use smoke test quickload, load this file file type.
Look at images in File Formats to make sure it is displayed correctly.
(need to add psl and pslx to quickload)
PSL file is not loaded in both 9.0.1 and 9.0.0
SymLoaderTabix.java

TwoBitNew.java

UnindexedSymLoader.java

VCF.java

Use smoke test quickload, load this file file type.
Look at images in File Formats to make sure it is displayed correctly.
Compared 9.0.0 VCF with current branch. Tallied Selection info. Looks good!
Wiggle.java

Use smoke test quickload, load this file file type.
Look at images in File Formats to make sure it is displayed correctly.
Looks good!
BAMSym.java

Use smoke test quickload, load this file file type.
Look at images in File Formats to make sure it is displayed correctly.
Looks good!
GeneralUtils.java

getURILength is never called and it has dependency imports of new library.(SeekableStream and SeekableStreamFactory) We need eliminate them and if method is not used then we need to delete it..
No major changes in file regarding new file.
LocalUrlCacher.java

No major code change. Only library updation in imports. Checked methods in API documentation of the library and the usage of them in the codebase.
Looks good!
SeekableBufferedStream.java

Only BAM.java uses SeekableBufferedStream of library. Everywhere else in the codebase, We have used customized SeekableBufferedStream file. Why?
Import change only.
SeekableFTPStream.java

Only import change. Doesn’t affect.
Looks Good!
core/shared-lib-wrapper/pom.xml

HttpDirectoryInputSeekableStream.java

Import change. Doesn’t affect the code
Looks Good!
ExonConnectorGlyph.java

One import change. Doesn’t affect.
Looks good!
TranscriptIsoformEvidenceVisualizationManager.java

Only import change. No major change.
Ivory please take a look.

main/pom.xml

plugins/bam/pom.xml

BAM.java

Use smoke test quickload, load this file file type.
Look at images in File Formats to make sure it is displayed correctly.
A doubt?
Looks Good!
Tested according to File Formats.
SAM.java

Use smoke test quickload, load this file file type.
Look at images in File Formats to make sure it is displayed correctly.

XAM.java

plugins/bed/pom.xml

BedSymloader.java
.bed file
Tested with Fileformat test page for .bed file. Compared Selection info of 9.0 to 9.0.1. Both matched. Import change in code file. No major change.
Looks Good!
plugins/external-sort/pom.xml

ExternalMergeSort.java

Import changed. Looked at the code. Does affect anything.
Looks Good!
pom.xml