[Help] Latest version of IGV fails to build

[Andreas Tille <andreas@an3as.eu>]

Hi,

I commited the packaging for last IGV to Git but it fails to build:

compile:
    [javac] /tmp/buildd/igv-2.3.34+dfsg/build.xml:175: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 864 source files to /tmp/buildd/igv-2.3.34+dfsg/tmp
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6
    [javac] /tmp/buildd/igv-2.3.34+dfsg/src/org/broad/igv/sam/SAMWriter.java:58: error: BAMFileWriter is not public in net.sf.samtools; cannot be accessed from outside package
    [javac]             writer = new BAMFileWriter(stream, null);
    [javac]                          ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 1 error
    [javac] 1 warning

BUILD FAILED


I guess for a Java-knowledged person this is easy to fix but I have no
idea how.  I also have the impression we could extend our
"Files-Excluded" to some more JARs which are distributed with IGV
source.

Feel free to fix and upload the package (or just commit a fix to Git and
tell me to upload)

       Andreas.

-- 
http://fam-tille.de