Bug#846708: FastQC should adapt to new htsjdk API which has dropped SAMFileReader (Was: [samtools/htsjdk] SAMFileReader vanished in Version 2.7.0 (#767))

Hi, I have uploaded biojava, do you still need i have a look? Seems sasha did the job.. :-) Olivier Le lun. 5 déc. 2016 22:24, olivier sallou a écrit : > Le lun. 5 déc. 2016 à 17:00, Andreas Tille a écrit : > > Hi folks, > > does anybody feel able

Bug#846708: FastQC should adapt to new htsjdk API which has dropped SAMFileReader (Was: [samtools/htsjdk] SAMFileReader vanished in Version 2.7.0 (#767))

Le lun. 5 déc. 2016 à 17:00, Andreas Tille a écrit : > Hi folks, > > does anybody feel able to rather patch FactQC than reintroducing the > outdated API to htsjdk? I have some work on biojava which requires quite a lot of patch updates for the moment, but after this I can try

Bug#846708: FastQC should adapt to new htsjdk API which has dropped SAMFileReader (Was: [samtools/htsjdk] SAMFileReader vanished in Version 2.7.0 (#767))

Hi folks, does anybody feel able to rather patch FactQC than reintroducing the outdated API to htsjdk? Same is valid for Artemis. I admit while reintroducing the old API works I'd consider this only the second best solution for the problem. Kind regards Andreas. On Mon, Dec 05, 2016 at

Bug#846708: FastQC should adapt to new htsjdk API which has dropped SAMFileReader (Was: [samtools/htsjdk] SAMFileReader vanished in Version 2.7.0 (#767))

Hi Andreas, None of the official FastQC releases has ever used htsjdk - we've been using the older picard sam.jar API which is substantially different (htsjdk is a major rewrite and restructure - it's not just a version update). Internally we have tried the new API, and although it works OK

Bug#846708: FastQC should adapt to new htsjdk API which has dropped SAMFileReader (Was: [samtools/htsjdk] SAMFileReader vanished in Version 2.7.0 (#767))

Hi Simon, after uploading htsjdk 2.7.0 FastQC 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