Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

merge devel to master, preparation for release 62.6 #396

Merged
merged 52 commits into from
Dec 13, 2016
Merged

merge devel to master, preparation for release 62.6 #396

merged 52 commits into from
Dec 13, 2016

Conversation

dozy
Copy link
Member

@dozy dozy commented Dec 12, 2016

No description provided.

mgcam and others added 30 commits September 20, 2016 10:51
@mgcam
consistent branch in Travis CI builds
01301a0
@mgcam
fix for dbix schema loader
ae75f6d
@mgcam
translation from a database composition representation to the npg_tra…
af68338 
…cking::glossary::composition type object
@mgcam
comments rearranged
6689246
@mgcam
collection search reimplemented - was implemented wrongly for composi…
7d31cb2 
…tions
@mgcam
add result role to SamtoolsStats DBIx object
855e060
@mgcam
typos fixed; tests for db-based results
c247331
@mgcam
Force comparison as numbers so 0 and 0.00 are considered equal
ca13c3b
@jmtcsngr
Merge pull request #376 from mgcam/test_fix
6f0f097 
test copes with loss of precision for zero values
@jmtcsngr
back to mysql 5.7.13
6618a1f
@mgcam @jmtcsngr
no templates rna_seqc results - we should not try rendering
c8576de
@mgcam @jmtcsngr
fix release number
e764ce6
@mgcam @jmtcsngr
Force comparison as numbers so 0 and 0.00 are considered equal
a7ebec0
@jmtcsngr
update Changes
f447b5a
@jmtcsngr
fix conflict in Changes
74741fd
@mgcam
Merge pull request #377 from jmtcsngr/mysql_5_7_13
6350b64 
Mysql 5 7 13
@jmtcsngr
drop node 0.12 & add perl 5.22-shrplib in travis
a78f8a7
@jmtcsngr
fixing tests after move to perl 22
7db4d1b
@mgcam
merged in wtsi/devel and resolved changes
7535710
@mgcam
beter version
4ce62bd
@mgcam
better change description
129c9e6
@mgcam
treat the perl-dnap-utilities package in line with other dependencies
7bfd192
@jmtcsngr
switch some for Undecided manual qc outcome
9af1b7a
@mgcam
Merge pull request #378 from jmtcsngr/perl_22
b0911fc 
Perl 22
@mgcam
move variable definition closer to where it is used
44a6901
@jmtcsngr
Merge pull request #359 from mgcam/follow_branch
6e006b4 
consistent branch in Travis CI builds
@mgcam
reduce uncertainty in ranking close results for teh old contamination…
45596a3 
… check
@jmtcsngr
Merge pull request #379 from mgcam/better_contam_comparison
ae94c0f 
reduce uncertainty in ranking close results
@mgcam
typo fixed
6ec01ca
@mgcam
merged in wtsi/devel and resolved conflict
b0bf5ea
dozy and others added 22 commits November 30, 2016 13:26
@dozy
call_gtck_composite_rpt.pl: supply rpt list to genotype check
1975777
@jenniferliddle
Merge pull request #381 from dozy/rpt_list_for_gtck
9e95d77 
call_gtck_composite_rpt.pl: supply rpt list to genotype check
@mgcam
fix SeqQC db query for composition-based tables
1677846
@mgcam
do not force numeric comparison on a potentially string argument
b859c56
@mgcam
PBP, BuiltinFunctions::ProhibitUselessTopic - Useless use of $_
ad06aab
@mgcam
proper NULL expression in YAML to avoid warnings when loading the dat…
08acc26 
…a to sqlite
@mgcam
Changes update
8639b21
@dkj
Merge pull request #384 from mgcam/perl5.22_fixes
ff25d8f 
Code and tests changes to reduce number of warnings under Perl 5.22.2
@mgcam
PDL return values fix
45ccb37
@mgcam
be very specific when dropping tag_index parameter from a query
6038b1e
@mgcam
Merge remote-tracking branch 'wtsi/devel' into rpt4composition
572c3d0
Use disposable-irods in Travis build; use perl-irods-wrap
d37bdce
@ces
Fix for rare out of order mpileup failures in genotype qc
5ca50f4
@dozy
Merge pull request #389 from ces/genosort
385fefa 
Fix for rare out of order mpileup failures in genotype qc
Merge pull request #388 from iainrb/irods_travis_and_interface_2
edb7620 
Use disposable-irods in Travis build; use perl-irods-wrap
@dkj
Merge pull request #385 from mgcam/pdl_return_values_fix
54ec786 
PDL return values fix: replace NaN/nan with undef
@kjsanger
Added -u to require initialised variables.
5af8343
Merge pull request #390 from keithj/initialise-variables
c45aa35 
Added -u to require initialised variables.
@dkj
Merge commit 'refs/pull/375/head' of https://github.com/wtsi-npg/npg_qc…
5944151 
… into devel

Conflicts:
	Changes
@dkj
Merge branch 'devel' of https://github.com/wtsi-npg/npg_qc into devel
f0ca881
@kjsanger
Made building the iRODS handle of npg_qc::autoqc::checks::genotype
3df99b2 
lazy to avoid calling baton until required at runtime.

Added WTSI::NPG::iRODS to Build.PL extended_requires.
@dozy
Merge pull request #395 from keithj/lazy-irods
3614434 
Made building the iRODS handle of npg_qc::autoqc::checks::genotype lazy
@dozy dozy merged commit b60d70c into master Dec 13, 2016
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
7 participants
@dozy @mgcam @jmtcsngr @jenniferliddle @dkj @ces @kjsanger