|
|
@3417
|
8 years |
Peter |
updating copyright statements
|
|
|
@3413
|
8 years |
Peter |
Prefer variable name HAVE_SAMTOOLS_EXECUTABLE instead of HAVE_SAMTOOLS …
|
|
|
@3412
|
8 years |
Peter |
throw exception rather than returnining empty string when ID or KEY is …
|
|
|
@3410
|
8 years |
Peter |
add two new functions read_group and program_group to access data in …
|
|
|
@3409
|
8 years |
Peter |
refs #817. Fix bug that struct was not updated in text(1) function (in …
|
|
|
@3408
|
8 years |
Peter |
Implement functions to get/set free text in BamHeader?. As setting the …
|
|
|
@3405
|
8 years |
Peter |
fixes #832
|
|
|
@3404
|
8 years |
Peter |
new function to reduce capacity in a vector
|
|
|
@3403
|
8 years |
Peter |
add constructor that takes compare functor
|
|
|
@3402
|
8 years |
Peter |
add interface to set priority of Scheduler::Job and make the order the …
|
|
|
@3401
|
8 years |
Peter |
refs #800
Avoid using parents and children terminologoy to describe …
|
|
|
@3400
|
8 years |
Peter |
refs #794
Deprecate configure option --without-samtools and add new …
|
|
|
@3399
|
8 years |
Peter |
closes #831; added new class PriorityQueue?.
|
|
|
@3395
|
8 years |
Peter |
closes #830. New function that calculates alignment_score of a bam …
|
|
|
@3394
|
8 years |
Peter |
remove static_test.sh. The test is identical with yat_m4_test.sh …
|
|
|
@3393
|
8 years |
Peter |
refs #803
The std::random_access_iterator promises that iterator …
|
|
|
@3390
|
8 years |
Peter |
extend comment
|
|
|
@3387
|
8 years |
Peter |
refs #803. MergeIterator?
|
|
|
@3384
|
8 years |
Peter |
closes #826
|
|
|
@3383
|
8 years |
Peter |
avoid tab in the middle of line
|
|
|
@3379
|
8 years |
Peter |
avoid using weighted_iterator_archetype with …
|
|
|
@3377
|
8 years |
Peter |
check that iterators are weighted
|
|
|
@3376
|
8 years |
Peter |
use weighted_iterator_traits in test for weighted_iterator_archetype
|
|
|
@3375
|
8 years |
Peter |
extend test
|
|
|
@3374
|
8 years |
Peter |
improve test diagnosis
|
|
|
@3373
|
8 years |
Peter |
remove empty lines
|
|
|
@3372
|
8 years |
Peter |
Fix bug in CigarIterator? that assumed BASE could be constructed from …
|
|
|
@3371
|
8 years |
Peter |
fix typo
|
|
|
@3369
|
8 years |
Peter |
make test compile in --without-samtools mode
|
|
|
@3365
|
8 years |
Peter |
Use pc from zlib and htslib when linking against those
packages. …
|
|
|
@3360
|
8 years |
Peter |
update copyright years
|
|
|
@3359
|
8 years |
Peter |
fix issues in OutBamFile::write. refs #794
|
|
|
@3356
|
8 years |
Peter |
refs #794. make test/pileup.cc compile with htslib
|
|
|
@3348
|
8 years |
Peter |
Replace Scheduler::launch() with a function Scheduler::wait(). Before …
|
|
|
@3347
|
8 years |
Peter |
remove protected function Scheduler::Job::submit. refs #800.
|
|
|
@3346
|
8 years |
Peter |
first version of Scheduler class. refs #800.
|
|
|
@3345
|
8 years |
Peter |
new function SegmentSet::insert_merge(first, last). closes #818
|
|
|
@3344
|
8 years |
Peter |
new function SegmentSet::insert_merge with hint. refs #818
|
|
|
@3342
|
8 years |
Peter |
merge 0.12.2 into trunk
|
|
|
@3336
|
8 years |
Peter |
closes #816
|
|
|
@3330
|
8 years |
Peter |
update copyright years
|
|
|
@3329
|
8 years |
Peter |
new class CigarIterator? that can be used to (surprise) iterate over a …
|
|
|
@3327
|
8 years |
Peter |
redefine Pileup::const_iterator so it avoids reads that do not overlap …
|
|
|
@3325
|
8 years |
Peter |
new functions phred and phred_inv that calculate phred scaled …
|
|
|
@3322
|
8 years |
Peter |
change name of test function to more descriptive …
|
|
|
@3317
|
8 years |
Peter |
refs #806 add test for Pileup class
|
|
|
@3315
|
8 years |
Peter |
added inclusion of boost iterator_facade header. refs #803.
|
|
|
@3314
|
8 years |
Peter |
new test class: weighted_iterator_archetype. refs #803
|
|
|
@3313
|
8 years |
Peter |
Correct syntax so it works in VPATH build. Correct yat-hello source so …
|
|
|
@3312
|
8 years |
Peter |
correct lazycheck deps
|
|
|
@3306
|
8 years |
Peter |
merge ptach release 0.12.1 into trunk
|
|
|
@3298
|
8 years |
Peter |
Yates' correction in Fisher's exact test. fixes #807.
|
|
|
@3295
|
9 years |
Peter |
merge release 0.12 into trunk
|
|
|
@3290
|
9 years |
Peter |
refs #803. Correct docs and reflect that random access iterators are …
|
|
|
@3289
|
9 years |
Peter |
refs #803. use boost concepts in Spearman.
|
|
|
@3287
|
9 years |
Peter |
new function sum_weight
|
|
|
@3285
|
9 years |
Peter |
refs #803. Use boost concepts in sort_index. Make requirements more …
|
|
|
@3283
|
9 years |
Peter |
remove trailing WS
|
|
|
@3281
|
9 years |
Peter |
Using boost concepts to define requirments in
Centralizer. …
|
|
|
@3280
|
9 years |
Peter |
avoid tabs on otherwise empty lines
|
|
|
@3273
|
9 years |
Peter |
refs #803. Extend iterator tests using boost concepts. For …
|
|
|
@3266
|
9 years |
Peter |
fixes #802
|
|
|
@3259
|
9 years |
Peter |
deprecated class Range. closes #786
|
|
|
@3255
|
9 years |
Peter |
removed repeat typedef
|
|
|
@3254
|
9 years |
Peter |
fixes #799
|
|
|
@3253
|
9 years |
Peter |
refs #799. get_error: don't use operator<< on Key just to create an …
|
|
|
@3251
|
9 years |
Peter |
remove WS
|
|
|
@3238
|
9 years |
Peter |
sort_index: add some compile tests, CONCEPT_ASSERTs, and add docs on …
|
|
|
@3236
|
9 years |
Peter |
BH correction on unsorted range. closes #796
|
|
|
@3228
|
9 years |
Peter |
test for YAT_HEADER_ASSERT
|
|
|
@3227
|
9 years |
Peter |
improve 'required' field. The tests use aclocal via the bootstrap …
|
|
|
@3213
|
9 years |
Peter |
three new cigar functions
|
|
|
@3210
|
9 years |
Peter |
update copyright years
|
|
|
@3209
|
9 years |
Peter |
add missing source file and fix compilation error --without-samtools
|
|
|
@3205
|
9 years |
Peter |
implement new class SmithWaterman?
|
|
|
@3201
|
9 years |
Peter |
add #define YAT_HAVE_LIBBAM to API and replace HAVE_LIBBAM accordingly.
|
|
|
@3200
|
9 years |
Peter |
implement first version of CIGAR (refs #785). Note, this revision does …
|
|
|
@3197
|
9 years |
Peter |
refs #790. workaround for old boost
|
|
|
@3196
|
9 years |
Peter |
avoid test code that won't compile with old boost.
|
|
|
@3194
|
9 years |
Peter |
add missing file. see r3173
|
|
|
@3190
|
9 years |
Peter |
new class KernelMatrix?. closes #381
|
|
|
@3188
|
9 years |
Peter |
merge patch release 0.11.2
|
|
|
@3177
|
9 years |
Peter |
Change behaviour if convert<T> and is<T> so they accept "-nan" (case …
|
|
|
@3175
|
9 years |
Peter |
new class BamPair?. refs #784
|
|
|
@3173
|
9 years |
Peter |
a first version of BamPairIterator?. refs #784
|
|
|
@3170
|
9 years |
Peter |
in yat-hello-check test that versions agree. refs #771.
|
|
|
@3162
|
9 years |
Peter |
refs #778. samwrite returns -1 if file is closed, so correct code to …
|
|
|
@3160
|
9 years |
Peter |
closes #775
|
|
|
@3152
|
9 years |
Peter |
add missing source file. refs #770
|
|
|
@3151
|
9 years |
Peter |
implement OstreamIterator? refs #770
|
|
|
@3150
|
9 years |
Peter |
test that BamWriteIterator? fulfills requirements defined in …
|
|
|
@3149
|
9 years |
Peter |
change test_output_iterator: there is requirement that output …
|
|
|
@3144
|
9 years |
Peter |
merge patch release 0.11.1 into trunk
|
|
|
@3138
|
9 years |
Peter |
change name of class and implement function llr(). closes #769
|
|
|
@3137
|
9 years |
Peter |
closes #772. new function that calculates mutual information
|
|
|
@3135
|
9 years |
Peter |
add function that calculates entropy from a range
|
|
|
@3134
|
9 years |
Peter |
refs #769 skeleton for new class LoglikelihoodRatioTestBinomial? (not …
|
|
|
@3130
|
9 years |
Peter |
merge release 0.11 into trunk
|
|
|
@3114
|
9 years |
Peter |
update copyright years
|
|
|
@3113
|
9 years |
Peter |
change YAT_USE_LIBTOOL_[PUSH|POP] so it only affects the linking tests …
|
|
|