|
|
@3417
|
8 years |
Peter |
updating copyright statements
|
|
|
@3415
|
8 years |
Peter |
refs #794
Change logic in configure test looking for libhts/samtools …
|
|
|
@3414
|
8 years |
Peter |
fix docs typo
|
|
|
@3412
|
8 years |
Peter |
throw exception rather than returnining empty string when ID or KEY is …
|
|
|
@3411
|
8 years |
Peter |
remove confusing reference to samtools API
|
|
|
@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 …
|
|
|
@3407
|
8 years |
Peter |
typo in comment
|
|
|
@3406
|
8 years |
Peter |
docs. refs #800
|
|
|
@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?.
|
|
|
@3398
|
8 years |
Peter |
refs #794
Global arrays bam_nt16_stable and bam_nt16_rev_table in …
|
|
|
@3397
|
8 years |
Peter |
fix regression introduced in r3287 (0.13pre).
|
|
|
@3396
|
8 years |
Peter |
include CigarIterator?.h in dist
|
|
|
@3395
|
8 years |
Peter |
closes #830. New function that calculates alignment_score of a bam …
|
|
|
@3393
|
8 years |
Peter |
refs #803
The std::random_access_iterator promises that iterator …
|
|
|
@3392
|
8 years |
Peter |
refs #803. sort_index
|
|
|
@3391
|
8 years |
Peter |
document requirements in SmithWaterman?. refs #803
|
|
|
@3389
|
8 years |
Peter |
docs
|
|
|
@3388
|
8 years |
Peter |
document requirements in MergeIterator?. refs #803
|
|
|
@3387
|
8 years |
Peter |
refs #803. MergeIterator?
|
|
|
@3386
|
8 years |
Peter |
remove trailing spaces
|
|
|
@3385
|
8 years |
Peter |
refs #803
|
|
|
@3384
|
8 years |
Peter |
closes #826
|
|
|
@3380
|
8 years |
Peter |
document how to access size of CIGAR array.
|
|
|
@3372
|
8 years |
Peter |
Fix bug in CigarIterator? that assumed BASE could be constructed from …
|
|
|
@3370
|
8 years |
Peter |
fix docs typo
|
|
|
@3368
|
8 years |
Peter |
add missing includes
|
|
|
@3363
|
8 years |
Peter |
improve docs. refs #794
|
|
|
@3362
|
8 years |
Peter |
avoid temp variable. refs #794
|
|
|
@3361
|
8 years |
Peter |
remove superfluous namespace
|
|
|
@3360
|
8 years |
Peter |
update copyright years
|
|
|
@3359
|
8 years |
Peter |
fix issues in OutBamFile::write. refs #794
|
|
|
@3358
|
8 years |
Peter |
fix how to read from a hts_itr_t. refs #794
|
|
|
@3357
|
8 years |
Peter |
refs #794. implement open and close functions
|
|
|
@3355
|
8 years |
Peter |
refs #794. implement BamRead::end() and BamRead::sequence() correctly …
|
|
|
@3353
|
8 years |
Peter |
refs #794. First version that compiles against htslib. Alibi …
|
|
|
@3352
|
8 years |
Peter |
implement BamHeader? against htslib, except parse region which requires …
|
|
|
@3351
|
8 years |
Peter |
make BamRead? compile with htslib. refs #794
|
|
|
@3350
|
8 years |
Peter |
Make configure htslib aware. Header detection changed to look for …
|
|
|
@3349
|
8 years |
Peter |
avoid having a std::set just to count number of jobs. refs #800
|
|
|
@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
|
|
|
@3337
|
8 years |
Peter |
use better hint; remove ws
|
|
|
@3336
|
8 years |
Peter |
closes #816
|
|
|
@3335
|
8 years |
Peter |
closes #806
|
|
|
@3334
|
8 years |
Peter |
Avoid stopping at position one passed a pile, instead fast forward to …
|
|
|
@3333
|
8 years |
Peter |
correct docs. refs #806
|
|
|
@3332
|
8 years |
Peter |
In Pileup store reads in a std::list (rather than std::deque) to allow …
|
|
|
@3330
|
8 years |
Peter |
update copyright years
|
|
|
@3329
|
8 years |
Peter |
new class CigarIterator? that can be used to (surprise) iterate over a …
|
|
|
@3328
|
8 years |
Peter |
avoid temporary variables; prefer initialization. refs #806
|
|
|
@3327
|
8 years |
Peter |
redefine Pileup::const_iterator so it avoids reads that do not overlap …
|
|
|
@3326
|
8 years |
Peter |
use same variable name (p) in docs as in argument list
|
|
|
@3325
|
8 years |
Peter |
new functions phred and phred_inv that calculate phred scaled …
|
|
|
@3324
|
8 years |
Peter |
grammar in comment
|
|
|
@3323
|
8 years |
Peter |
prefer strcmp over generic std::equal
|
|
|
@3322
|
8 years |
Peter |
change name of test function to more descriptive …
|
|
|
@3320
|
8 years |
Peter |
speedup. assume Distance is symmetric. closes #814
|
|
|
@3319
|
8 years |
Peter |
avoid long line
|
|
|
@3318
|
8 years |
Peter |
closes #813
|
|
|
@3317
|
8 years |
Peter |
refs #806 add test for Pileup class
|
|
|
@3316
|
8 years |
Peter |
remove trailing ws
|
|
|
@3310
|
8 years |
Peter |
a first version of new class Pileup. refs #806
|
|
|
@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.
|
|
|
@3297
|
8 years |
Peter |
fix mess up caused in latest merge (r3295).
|
|
|
@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.
|
|
|
@3288
|
9 years |
Peter |
add doxygen since tag
|
|
|
@3287
|
9 years |
Peter |
new function sum_weight
|
|
|
@3286
|
9 years |
Peter |
fixed docs typo
|
|
|
@3285
|
9 years |
Peter |
refs #803. Use boost concepts in sort_index. Make requirements more …
|
|
|
@3282
|
9 years |
Peter |
avoid extra tabs
|
|
|
@3281
|
9 years |
Peter |
Using boost concepts to define requirments in
Centralizer. …
|
|
|
@3279
|
9 years |
Peter |
use boost_concepts requirements in random namespace. refs #803
|
|
|
@3278
|
9 years |
Peter |
use boost concept requirements in random namespace. refs #803
|
|
|
@3276
|
9 years |
Peter |
ref #803. revert part of r3273 for the same reason as explained in r3275
|
|
|
@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
|
|
|
@3258
|
9 years |
Peter |
correct docs of YAT_DEV_BUILD
|
|
|
@3257
|
9 years |
Peter |
added missing deprecated attribute
|
|
|
@3254
|
9 years |
Peter |
fixes #799
|
|
|
@3253
|
9 years |
Peter |
refs #799. get_error: don't use operator<< on Key just to create an …
|
|
|
@3252
|
9 years |
Peter |
avoid split in Codon
|
|
|
@3249
|
9 years |
Peter |
mention Deleter in SmartPtr? doc
|
|
|
@3247
|
9 years |
Peter |
docs: fixed typo in example code
|
|
|
@3245
|
9 years |
Peter |
avoid sorting entire range; instead let Percentiler be clever
|
|
|