

@4057

2 years 
Peter 
closes #798; new classes BamPairBuffer? and a more general SortedBuffer?.



@4056

2 years 
Peter 
docs: fix typo and add clarification



@4055

2 years 
Peter 
remove unneeded includes



@4054

2 years 
Peter 
mention modified interface in previous commit



@4053

2 years 
Peter 
add some test for correlation(Matrix); speed up, particuarly when …



@4052

2 years 
Peter 
add description on what is optimised during the training.



@4051

2 years 
Peter 
make Target::classifier() const; closes #972



@4050

2 years 
Peter 
remove whitespace



@4049

2 years 
Peter 
do not allow implicit conversion



@4048

2 years 
Peter 
add parameter allowing scaling to other than unity variance.



@4047

2 years 
Peter 
corrected includes



@4046

2 years 
Peter 
docs typo



@4045

2 years 
Peter 
add missing file



@4044

2 years 
Peter 
new function multiprocess; closes #958



@4043

2 years 
Peter 
Add capacity to Queue and PriorityQueue?, which is a feature to limit …



@4042

2 years 
Peter 
upgrade to autoconfarchive2021.02.19



@4041

2 years 
Peter 
avoid constructing temporary substring just for comparison



@4040

2 years 
Peter 
speedup; prefer move instead of copy



@4039

2 years 
Peter 
Using me::value_type propagated to compilation errors and created …



@4038

2 years 
Peter 
merge trunk into branch



@4037

2 years 
Peter 
skeleton for new Ranking container. refs #710.



@4036

2 years 
Peter 
closes #963. New class PercentileConfidenceInterval?



@4035

2 years 
Peter 
skeleton for PercentileConfidenceInterval?; refs #963



@4034

2 years 
Peter 
Decouple variables for extra programs and test programs, to allow …



@4033

2 years 
Peter 
bumping version to 0.18.2pre



@4032

2 years 
Peter 
merge release 0.18.1 into trunk



@4031

2 years 
Peter 
tagging version 0.18.1



@4030

2 years 
Peter 
preparing release 0.18.1



@4029

2 years 
Peter 
extend the tests show what the comparison functors take as argument; …



@4028

2 years 
Peter 
fixes #970



@4027

2 years 
Peter 
refs #968; fix implementation of SegmentSet::insert_merge and add some …



@4026

2 years 
Peter 
add rvalue insert to SegmentSet?; closes #968.



@4025

2 years 
Peter 
add move constructor for BamPair?



@4024

2 years 
Peter 
refs #968; SegmentTree::insert taking rvalue



@4023

2 years 
Peter 
refs #968; Segment constrctor taking rvalues



@4022

2 years 
Peter 
prefer std::shared_ptr over boost



@4021

2 years 
Peter 
closes #961. Improve message in thrown exceptions.



@4020

2 years 
Peter 
bump version to 0.18.1pre



@4019

2 years 
Peter 
merge 0.18 into trunk



@4018

2 years 
Peter 
tagging version 0.18



@4017

2 years 
Peter 
correct date format



@4016

2 years 
Peter 
updating copyright years



@4015

2 years 
Peter 
Preparing release 0.18



@4014

2 years 
Peter 
prefer std::shared_ptr over boost



@4013

2 years 
Peter 
fix test failure when srcdir was absolute path



@4012

2 years 
Peter 
../$(scrdir) does not work when srcdir is an absolute path



@4011

2 years 
Peter 
Use std smart pointers instead of boost. Prefer initialisation of …



@4010

2 years 
Peter 
Implement move constructo and moveassignment operator for …



@4009

2 years 
Peter 
closes #965; Default constructor for DiscreteGeneral?



@4008

2 years 
Peter 
Remove Distribution class and its daughter classes. It used …



@4007

2 years 
Peter 
There was a typo that yat_result was first set to "non required" and …



@4006

2 years 
Peter 
fix bug that doxygen.config was not updated when set of input files …



@4005

2 years 
Peter 
int8_t needs <cstdint> when sam.h isn't included



@4004

2 years 
Peter 
add \since tag for new exception class invalid_argument



@4003

2 years 
Peter 
Add a constructor Aligner::Cigar(string) (closes #962)
Add a function …



@4002

2 years 
Peter 
Creating a private branch for refactoring of KendallScore? (refs #710)



@4001

2 years 
Peter 
Bumping version to 0.19pre



@4000

2 years 
Peter 
New stable branch 0.18



@3999

2 years 
Peter 
update copyright years



@3998

2 years 
Peter 
Prepare 0.18stable branch



@3997

2 years 
Peter 
merge 0.17stable branch into trunk



@3996

2 years 
Peter 
prefer std smart pointers



@3995

3 years 
Peter 
avoid using macros marked obsolete and instead use versions in LT_ …



@3994

3 years 
Peter 
simplify code



@3993

3 years 
Peter 
simplify code



@3992

3 years 
Peter 
recommend std rather than boost



@3991

3 years 
Peter 
new constructor in GenomicPosition?



@3990

3 years 
Peter 
prefer name with 'htslib' (instead of 'samtools')



@3989

3 years 
Peter 
there is no default sf_user; make the text reflect that.



@3988

3 years 
Peter 
bumping version to 0.17.3pre



@3987

3 years 
Peter 
merge release 0.17.2 into trunk



@3986

3 years 
Peter 
tagging version 0.17.2



@3985

3 years 
Peter 
update copyright years



@3984

3 years 
Peter 
Preparing release 0.17.2



@3983

3 years 
Peter 
remove some text not relevant anymore, when we assume c++11 and htslib



@3982

3 years 
Peter 
improve docs



@3981

3 years 
Peter 
cater for c++98



@3980

3 years 
Peter 
fixes #957. NegativeBinomial? now inherits from Multivariate



@3979

3 years 
Peter 
fix distcheck (refs #954)



@3978

3 years 
Peter 
leftover (refs #954)



@3977

3 years 
Peter 
avoid accessing passed matrix (Ain) after it has been moved.



@3976

3 years 
Peter 
mention #955 in NEWS



@3975

3 years 
Peter 
fixes #955.
The correction term involving count_triple() was not …



@3974

3 years 
Peter 
remove a dead declaration in test::SUite class and improve docs of …



@3973

3 years 
Peter 
add dependency for lazycheck (refs #955)



@3972

3 years 
Peter 
add test data for statistics::Kendall (refs #955)



@3971

3 years 
Peter 
fixes #956. Vector::resize(0) did not work when the vector was …



@3970

3 years 
Peter 
explain what position is when inside an insertion



@3969

3 years 
Peter 
docs typo



@3968

3 years 
Peter 
merge r3967 into trunk



@3967

3 years 
Peter 
fix leftover issues for r3965 (refs #954) caught by distcheck: …



@3966

3 years 
Peter 
merge changes in 0.17stable branch (since 0.17.1) into trunk.



@3965

3 years 
Peter 
fixes #954. Avoid reading config file from stdin with doxygen.



@3964

3 years 
Peter 
avoid warning with doxygen 1.8.19



@3963

3 years 
Peter 
new function supposed to be used by GSL error handler, resulting in a …



@3962

3 years 
Peter 
a4wide used to be the default value for PAPER_TYPE. but with modern …



@3961

3 years 
Peter 
fixes #845. Replace default GSL error handler in tests with one that …



@3960

3 years 
Peter 
closes #953. Since we are no longer using libboost_thread (or …



@3959

3 years 
Peter 
use std::mutex and friends instead of boost variants. refs #953



@3958

3 years 
Peter 
change to using std distributions instead of boost. Some distributions …


