Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 694d8c85551013a894a491d4be9e5a46b72fb199 https://github.com/galaxyproject/galaxy/commit/694d8c85551013a894a491d4be9e5... Author: Devon Ryan dpryan79@gmail.com Date: 2017-06-26 (Mon, 26 Jun 2017)

Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Sniff FastqSanger before Fastq, in the former case checking the quality scores for compatibility

Commit: 0a942d79a326c3b2cfb8d7cbee6a341e4600a77f https://github.com/galaxyproject/galaxy/commit/0a942d79a326c3b2cfb8d7cbee6a3... Author: Devon Ryan dpryan79@gmail.com Date: 2017-06-26 (Mon, 26 Jun 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Checking the quality lines will make fastqsanger checks rather more relevant.

Commit: bc13a16f83d9d74774751fbe5c4d7d3b2b3c6ecc https://github.com/galaxyproject/galaxy/commit/bc13a16f83d9d74774751fbe5c4d7... Author: Devon Ryan dpryan79@gmail.com Date: 2017-06-26 (Mon, 26 Jun 2017)

Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Add the compressed datatypes to the sniffer lsit

Commit: ab1127334f1c0e2d43c4fcccb9259c33fdaf235b https://github.com/galaxyproject/galaxy/commit/ab1127334f1c0e2d43c4fcccb9259... Author: Devon Ryan dpryan79@gmail.com Date: 2017-06-27 (Tue, 27 Jun 2017)

Changed paths: M lib/galaxy/datatypes/registry.py

Log Message: ----------- Remove debugging stuff, since everything works inside of docker

Commit: 798b73eb688c5b7786fe2b9ffe69967ded3d7c63 https://github.com/galaxyproject/galaxy/commit/798b73eb688c5b7786fe2b9ffe699... Author: Devon Ryan dpryan79@gmail.com Date: 2017-06-27 (Tue, 27 Jun 2017)

Changed paths: M lib/galaxy/datatypes/registry.py

Log Message: ----------- Fix line reordering

Commit: 8eaede31102b16f09abcbc8f0f06c6eab75d49bb https://github.com/galaxyproject/galaxy/commit/8eaede31102b16f09abcbc8f0f06c... Author: Devon Ryan dpryan79@gmail.com Date: 2017-06-27 (Tue, 27 Jun 2017)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Fix sequence.py unit test

Commit: f3853a09562af8d7539740344433c4a8dc94aa36 https://github.com/galaxyproject/galaxy/commit/f3853a09562af8d7539740344433c... Author: Devon Ryan dpryan79@gmail.com Date: 2017-06-27 (Tue, 27 Jun 2017)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Test a non-fastqsanger file and ensure it doesn't pass the sniff test.

Commit: 907bd53776eccec0e8d3fadfb69223dadcc48600 https://github.com/galaxyproject/galaxy/commit/907bd53776eccec0e8d3fadfb6922... Author: Devon Ryan dpryan79@gmail.com Date: 2017-06-27 (Tue, 27 Jun 2017)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Make the phred range stricter and more explicit.

Commit: e21e9ec15fec5d3d1e47cd3c3001d9be24fbf12c https://github.com/galaxyproject/galaxy/commit/e21e9ec15fec5d3d1e47cd3c3001d... Author: Devon Ryan dpryan79@gmail.com Date: 2017-06-27 (Tue, 27 Jun 2017)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Ugh, there were multiple places where the sniffing order was specified (binary formats are different).

Commit: 6cd026bc7b32866437ca6e4e996e0cddeb40f837 https://github.com/galaxyproject/galaxy/commit/6cd026bc7b32866437ca6e4e996e0... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-06-28 (Wed, 28 Jun 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Merge pull request #4237 from dpryan79/fastqSniffer_implement3571

Sniff fastqsanger and prefer it over fastq if the quality scores match

Compare: https://github.com/galaxyproject/galaxy/compare/e98378160a46...6cd026bc7b32