Timeline



Dec 3, 2014:

12:23 PM Ticket #808 (prefer using .private variable (when possible) in yat.pc) closed by Peter
fixed: (In [3366]) prefer private variables in yat.pc. closes #808
12:23 PM Changeset [3366] by Peter
prefer private variables in yat.pc. closes #808

Dec 1, 2014:

12:14 PM Ticket #809 (use zlib's pc file) closed by Peter
fixed: (In [3365]) Use pc from zlib and htslib when linking against those …
12:14 PM Changeset [3365] by Peter
Use pc from zlib and htslib when linking against those packages. …

Nov 25, 2014:

2:17 PM Changeset [3364] by Peter
describe htslib support in NEWS and README. refs #794
11:42 AM Changeset [3363] by Peter
improve docs. refs #794
11:41 AM Changeset [3362] by Peter
avoid temp variable. refs #794

Nov 24, 2014:

7:35 AM Changeset [3361] by Peter
remove superfluous namespace
2:22 AM Changeset [3360] by Peter
update copyright years

Nov 23, 2014:

1:05 PM Changeset [3359] by Peter
fix issues in OutBamFile::write. refs #794
8:02 AM Changeset [3358] by Peter
fix how to read from a hts_itr_t. refs #794
2:54 AM Changeset [3357] by Peter
refs #794. implement open and close functions

Nov 22, 2014:

2:34 PM Changeset [3356] by Peter
refs #794. make test/pileup.cc compile with htslib
2:17 PM Changeset [3355] by Peter
refs #794. implement BamRead::end() and BamRead::sequence() correctly …
12:59 PM Changeset [3354] by Peter
refs #794. fix configure test so it works with htslib.
11:26 AM Changeset [3353] by Peter
refs #794. First version that compiles against htslib. Alibi …
12:16 AM Changeset [3352] by Peter
implement BamHeader? against htslib, except parse region which requires …

Nov 21, 2014:

1:20 PM Changeset [3351] by Peter
make BamRead? compile with htslib. refs #794

Nov 20, 2014:

2:25 PM Changeset [3350] by Peter
Make configure htslib aware. Header detection changed to look for …

Nov 13, 2014:

4:59 AM Changeset [3349] by Peter
avoid having a std::set just to count number of jobs. refs #800
2:12 AM Changeset [3348] by Peter
Replace Scheduler::launch() with a function Scheduler::wait(). Before …

Nov 9, 2014:

7:46 AM Changeset [3347] by Peter
remove protected function Scheduler::Job::submit. refs #800.

Nov 6, 2014:

2:16 PM Changeset [3346] by Peter
first version of Scheduler class. refs #800.
1:30 PM Ticket #818 (SegmentSet::insert_merge(range)) closed by Peter
fixed: (In [3345]) new function SegmentSet::insert_merge(first, last). closes #818
1:30 PM Changeset [3345] by Peter
new function SegmentSet::insert_merge(first, last). closes #818
1:09 PM Changeset [3344] by Peter
new function SegmentSet::insert_merge with hint. refs #818
6:31 AM Changeset [3343] by Peter
bumping version to 0.12.3pre
6:26 AM Changeset [3342] by Peter
merge 0.12.2 into trunk
6:18 AM Milestone yat 0.12.2 completed
bugfix release - unexpected CIGAR - QuantileNormalizer? segfaults if …
6:18 AM SubversionCheckout edited by Peter
(diff)
6:17 AM WikiStart edited by Peter
(diff)
5:58 AM Changeset [3341] by Peter
tagging version 0.12.2
5:39 AM Changeset [3340] by Peter
Preparing release 0.12.2
12:43 AM Ticket #820 (Unexpected CIGAR) closed by Peter
fixed: (In [3339]) Fix problem that Aligner::member_ is not cleared to 'none' …
12:43 AM Changeset [3339] by Peter
Fix problem that Aligner::member_ is not cleared to 'none' before …

Nov 5, 2014:

1:10 PM Ticket #819 (SmithWaterman::operator()(4)) closed by Peter
fixed: (In [3338]) closes #819. Fixes docs.
1:10 PM Changeset [3338] by Peter
closes #819. Fixes docs.
7:35 AM Ticket #820 (Unexpected CIGAR) created by Peter
I use Smithwaterman to align a query against ref as below with gap=2, …

Nov 4, 2014:

9:03 AM Ticket #819 (SmithWaterman::operator()(4)) created by Peter
operator is declared as […] but if I call it with […] I get …
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