Timeline



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 …

Oct 27, 2014:

2:46 PM Changeset [3337] by Peter
use better hint; remove ws
8:16 AM Ticket #818 (SegmentSet::insert_merge(range)) created by Peter
Is there any reason there is no insert_merge that takes a (sorted) range?
6:57 AM Ticket #817 (access misc text in BamHeader) created by Peter
Current interface (0.12) can only translate tid to chromosome number …

Oct 25, 2014:

1:27 AM Ticket #816 (create CigarIterator from Aligner::Cigar) closed by Peter
fixed: (In [3336]) closes #816
1:27 AM Changeset [3336] by Peter
closes #816

Oct 24, 2014:

2:27 AM Ticket #816 (create CigarIterator from Aligner::Cigar) created by Peter
Add iterator interface to Aligner::Cigar with functions: […] where …

Oct 23, 2014:

4:33 PM Ticket #806 (bam pileup) closed by Peter
fixed: (In [3335]) closes #806
4:33 PM Changeset [3335] by Peter
closes #806
3:26 PM Changeset [3334] by Peter
Avoid stopping at position one passed a pile, instead fast forward to …
2:26 PM Changeset [3333] by Peter
correct docs. refs #806
1:18 PM Changeset [3332] by Peter
In Pileup store reads in a std::list (rather than std::deque) to allow …

Oct 17, 2014:

1:45 AM Changeset [3331] by Peter
update to autoconf-archive 2014.10.15

Oct 14, 2014:

10:03 AM Changeset [3330] by Peter
update copyright years

Oct 12, 2014:

10:25 AM Changeset [3329] by Peter
new class CigarIterator? that can be used to (surprise) iterate over a …

Oct 10, 2014:

1:41 PM Changeset [3328] by Peter
avoid temporary variables; prefer initialization. refs #806
10:30 AM Changeset [3327] by Peter
redefine Pileup::const_iterator so it avoids reads that do not overlap …

Oct 8, 2014:

3:30 AM Changeset [3326] by Peter
use same variable name (p) in docs as in argument list

Oct 7, 2014:

3:44 AM Changeset [3325] by Peter
new functions phred and phred_inv that calculate phred scaled …
12:56 AM Changeset [3324] by Peter
grammar in comment
12:55 AM Changeset [3323] by Peter
prefer strcmp over generic std::equal
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