SAMFileReader vanished in Version 2.7.0

[tillea]

Hi,
since htsjdk was uploaded to Debian the packages fastqc and artemis do not build any more with the very same problem which can be seen in the Debian bug tracking system ( fastqc, artemis ) where you have the build logs which end both by something like

/<>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamUtils.java:190: error: cannot find symbol
SAMFileReader inputSam = samFileReaderHash.get(bamFile);
^
symbol: class SAMFileReader
location: class BamUtils

I checked that htsjdk is featuring SAMFileReader in the file src/main/java/htsjdk/samtools/SAMFileReader.java - but it just vanished from there.

Your environment

• version 2.7.0 of htsjdk
• version of java: openjdk-8-jdk 8u111
• Debian (unstable) - trying to build fastqc and artemis package

Steps to reproduce

Please try to build fastqc.

Kind regards, Andreas.

[tillea]

Hi again,
I simply tried to add a copy of src/main/java/htsjdk/samtools/SAMFileReader.java from htsjdk 2.6.1 in 2.7.0, rebuild the Debian package with this. If I now build fastqc everything seems to be fine. Did you possibly removed the file by accident and it just needs to be restored?
Kind regards, Andreas.

[magicDGS]

The file was removed in #699 because it was deprecated. I guess that either 1) fastqc/artemis should be updated to use the new API version, or 2) the classpath for them in Debian should include an older version.

[lbergelson]

closing, feel free to reopen a new issue if you need help migrating to the new code