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

Hi all, [...] > I do not find branch 6_0_17 and I do not even think that we need this > extra branch. I'd recommend to use master and as far as I understood > Olivier's comment your test should be sufficient. Sure. Sorry for the branch naming mixup, it was a little late ;) > I personally also

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

Hi Sascha, Thanks a million for patching this issue. Regards, Andrew > On 8 Dec 2016, at 08:11, Andreas Tille wrote: > > Ahh, I've found branch 6_0_17_fix - I can do the merge ... > > On Thu, Dec 08, 2016 at 09:06:52AM +0100, Andreas Tille wrote: >> Hi Sascha, >> >> On

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

Ahh, I've found branch 6_0_17_fix - I can do the merge ... On Thu, Dec 08, 2016 at 09:06:52AM +0100, Andreas Tille wrote: > Hi Sascha, > > On Thu, Dec 08, 2016 at 01:04:34AM +0100, Sascha Steinbiss wrote: > > to address this problem I have taken a shot at patching Debian’s Artemis to > > use

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

Hi Sascha, On Thu, Dec 08, 2016 at 01:04:34AM +0100, Sascha Steinbiss wrote: > 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

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

Le jeu. 8 déc. 2016 01:04, Sascha Steinbiss a écrit : > 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

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

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