<br><br><div class="gmail_quote"><div dir="ltr">Le jeu. 8 déc. 2016 01:04, Sascha Steinbiss <<a href="mailto:satta@tetrinetsucht.de">satta@tetrinetsucht.de</a>> a écrit :<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Andreas and Andrew,<br class="gmail_msg">
<br class="gmail_msg">
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.<br class="gmail_msg">
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.<br class="gmail_msg"></blockquote></div><div>If you compile and can view the bam, i would consider the api call is correct and so your patch</div><div><br></div><div>Olivier</div><div><br></div><div><br></div><div><br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br class="gmail_msg">
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.<br class="gmail_msg">
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.<br class="gmail_msg">
<br class="gmail_msg">
Cheers<br class="gmail_msg">
Sascha<br class="gmail_msg">
<br class="gmail_msg">
> On 5 Dec 2016, at 15:56, Andrew Page <<a href="mailto:ap13@sanger.ac.uk" class="gmail_msg" target="_blank">ap13@sanger.ac.uk</a>> wrote:<br class="gmail_msg">
><br class="gmail_msg">
> Hi Andreas,<br class="gmail_msg">
> 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!<br class="gmail_msg">
> Regards,<br class="gmail_msg">
> Andrew<br class="gmail_msg">
><br class="gmail_msg">
><br class="gmail_msg">
><br class="gmail_msg">
>> On 5 Dec 2016, at 14:40, Andreas Tille <<a href="mailto:tille@debian.org" class="gmail_msg" target="_blank">tille@debian.org</a>> wrote:<br class="gmail_msg">
>><br class="gmail_msg">
>> Hi,<br class="gmail_msg">
>><br class="gmail_msg">
>> after uploading htsjdk 2.7.0 Artemis failed to build from source[1]. I<br class="gmail_msg">
>> relised that the file src/main/java/htsjdk/samtools/SAMFileReader.java<br class="gmail_msg">
>> was removed from htsjdk source and assumed that this was by accident.<br class="gmail_msg">
>> However, upstream has dropped this interface intentionally as you can<br class="gmail_msg">
>> read below. In issue #767[2] an htsjdk author gives advise to use the<br class="gmail_msg">
>> new API version.<br class="gmail_msg">
>><br class="gmail_msg">
>> Kind regards<br class="gmail_msg">
>><br class="gmail_msg">
>> Andreas.<br class="gmail_msg">
>><br class="gmail_msg">
>><br class="gmail_msg">
>> [1] <a href="https://bugs.debian.org/846671" rel="noreferrer" class="gmail_msg" target="_blank">https://bugs.debian.org/846671</a><br class="gmail_msg">
>> [2] <a href="https://github.com/samtools/htsjdk/issues/767" rel="noreferrer" class="gmail_msg" target="_blank">https://github.com/samtools/htsjdk/issues/767</a><br class="gmail_msg">
>><br class="gmail_msg">
>><br class="gmail_msg">
>> ----- Forwarded message from Daniel Gómez-Sánchez <<a href="mailto:notifications@github.com" class="gmail_msg" target="_blank">notifications@github.com</a>> -----<br class="gmail_msg">
>><br class="gmail_msg">
>> Date: Mon, 05 Dec 2016 06:18:16 -0800<br class="gmail_msg">
>> From: Daniel Gómez-Sánchez <<a href="mailto:notifications@github.com" class="gmail_msg" target="_blank">notifications@github.com</a>><br class="gmail_msg">
>> To: samtools/htsjdk <<a href="mailto:htsjdk@noreply.github.com" class="gmail_msg" target="_blank">htsjdk@noreply.github.com</a>><br class="gmail_msg">
>> Cc: Andreas Tille <<a href="mailto:tille@debian.org" class="gmail_msg" target="_blank">tille@debian.org</a>>, Author <<a href="mailto:author@noreply.github.com" class="gmail_msg" target="_blank">author@noreply.github.com</a>><br class="gmail_msg">
>> Subject: Re: [samtools/htsjdk] SAMFileReader vanished in Version 2.7.0 (#767)<br class="gmail_msg">
>><br class="gmail_msg">
>> 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.<br class="gmail_msg">
>><br class="gmail_msg">
>> --<br class="gmail_msg">
>> You are receiving this because you authored the thread.<br class="gmail_msg">
>> Reply to this email directly or view it on GitHub:<br class="gmail_msg">
>> <a href="https://github.com/samtools/htsjdk/issues/767#issuecomment-264864910" rel="noreferrer" class="gmail_msg" target="_blank">https://github.com/samtools/htsjdk/issues/767#issuecomment-264864910</a><br class="gmail_msg">
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