[Debian-med-packaging] Bug#846671: Bug#846671: Artemis should adapt to new htsjdk API which has dropped SAMFileReader (Was: [samtools/htsjdk] SAMFileReader vanished in Version 2.7.0 (#767))]

[Sascha Steinbiss]

Hi Andreas and Andrew,

to address this problem I have taken a shot at patching Debian’s Artemis to use the new htsjdk API, avoiding SAMFileReader and using the SamReaderFactory instead. This fixed the FTBFS for me.
I tested BAM file reading by opening MAL1.embl.gz from the test/data directory and adding MAL1_8h.bam via ‘File->Read BAM/VCF...'. One of the genes has some mapped reads that are indeed shown. Comparing the displayed pile of mapped reads to the one shown by the recent Artemis version I have on Mac OS X, the result seems to be correct, but given my lack of practical experience with the BAM/VCF/‘anything-to-do-with-reads' components of Artemis I can’t say if I caught everything.

I also updated the Debian version to 16.0.17, the latest release from Sanger. This allowed me to drop a couple of patches that I already merged earlier with my part-time-upstream hat on.
For now I have pushed my work into the ’6_0_17’ branch in git and I would like to kindly ask for some more testing. I don’t have suitable test data here and don’t really feel like an expert to test the right usage patterns. 

Cheers
Sascha

> On 5 Dec 2016, at 15:56, Andrew Page <ap13 at sanger.ac.uk> wrote:
> 
> Hi Andreas,
> Thanks for letting us know.  We are actively trying to hire a Java developer who will take over the maintenance and development of Artemis. So unfortunately it will be at least a few months before we will have anyone in post to work on it.  If you happen to know of anyone looking for a job, please send them our way!
> Regards,
> Andrew
> 
> 
> 
>> On 5 Dec 2016, at 14:40, Andreas Tille <tille at debian.org> wrote:
>> 
>> Hi,
>> 
>> after uploading htsjdk 2.7.0 Artemis failed to build from source[1].  I
>> relised that the file src/main/java/htsjdk/samtools/SAMFileReader.java
>> was removed from htsjdk source and assumed that this was by accident.
>> However, upstream has dropped this interface intentionally as you can
>> read below.  In issue #767[2] an htsjdk author gives advise to use the
>> new API version.
>> 
>> Kind regards
>> 
>>      Andreas.
>> 
>> 
>> [1] https://bugs.debian.org/846671
>> [2] https://github.com/samtools/htsjdk/issues/767
>> 
>> 
>> ----- Forwarded message from Daniel Gómez-Sánchez <notifications at github.com> -----
>> 
>> Date: Mon, 05 Dec 2016 06:18:16 -0800
>> From: Daniel Gómez-Sánchez <notifications at github.com>
>> To: samtools/htsjdk <htsjdk at noreply.github.com>
>> Cc: Andreas Tille <tille at debian.org>, Author <author at noreply.github.com>
>> Subject: Re: [samtools/htsjdk] SAMFileReader vanished in Version 2.7.0 (#767)
>> 
>> 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.
>> 
>> -- 
>> You are receiving this because you authored the thread.
>> Reply to this email directly or view it on GitHub:
>> https://github.com/samtools/htsjdk/issues/767#issuecomment-264864910
>> 
>> ----- End forwarded message -----
>> 
>> -- 
>> http://fam-tille.de
>> 
>> ----- End forwarded message -----
>> 
>> -- 
>> http://fam-tille.de
> 
> 
> 
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