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bio
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330 Коммитов

Автор SHA1 Сообщение Дата
Nigel Delaney dc922c7d9b Merge pull request #9 from dotnetbio/fixoffset 
Fix indexing error in DNA sequence validation step. Before we would index from i = start to i < length, but the way the comments were written we should have gone from i = start to i < (start + length)
 2015-12-02 19:55:02 -08:00
Nigel Delaney 27187d55f5 Fix indexing error in validation step. 2015-12-02 19:43:18 -08:00
Nigel Delaney b4159816cd Merge branch 'master' of https://github.com/dotnetbio/bio 2015-11-01 22:10:48 -08:00
Nigel Delaney e9d6038f9b Avoid overwriting PQ flag with RQ if present 2015-11-01 22:10:21 -08:00
Nigel Delaney 1db97fd9c2 Merge pull request #7 from jjby/master 
Make the GenBank parser more robust to different indentations of the ORIGIN
 2015-10-23 01:57:12 -07:00
Jakob Jakobsen Boysen 56aa00aef6 Make the GenBank parser more robust to different indentations of the ORIGIN. 2015-10-22 16:35:30 +02:00
Nigel Delaney 00270f4c04 Fix Travis CI File 2015-10-14 12:49:06 -07:00
Nigel Delaney 543f843e47 Fix BioTools build 2015-10-14 12:43:13 -07:00
Nigel Delaney 721e106a94 Fix the tests 2015-10-14 12:15:20 -07:00
Nigel Delaney c4c1640c9c Update CCS Read Parser 
* pq flag replaced with rq
* ReadCountMemFail no longer reported
* Update test data
 2015-10-14 11:48:10 -07:00
Nigel Delaney db7e581c28 Test Bio.Tools can build X-Plat 2015-10-12 18:43:08 -07:00
Nigel Delaney 3b7f0320b8 Allow Bio.Tools to Build X-Platform 
Allow Bio.Tools to build X-Platform

Three changes

* Removed XML from build scripts seeking to restore nuget targets
* Changed packages.config files to work around case sensitive issue
(NetBio -> NETBio)
* Removed a few variables that were not used, causing Warning as Error
failures.
 2015-10-12 18:33:15 -07:00
Nigel Delaney de814a1108 Change SNPVariant to support AtEnd Feature 2015-08-22 13:53:31 -07:00
Nigel Delaney f1486bedba Fix Typo 2015-08-07 17:51:40 -07:00
Nigel Delaney a3cd0b9762 Replace integer RQ with float RQ 
Also implement ISequence and IQualitativeSequence on PacBioCCSRead for
convenience.
 2015-08-07 16:36:46 -07:00
Nigel Delaney 1d2b018818 Add more detailed alignment exception information. 2015-08-07 16:35:28 -07:00
Nigel Delaney 2a6d36fcd6 Add note on QV for deletion mutations. 2015-08-07 16:34:58 -07:00
Nigel Delaney 4f207b370a Merge pull request #2 from dotnetbio/variantcaller 
Add Bio.Variant Namespace
 2015-08-04 19:43:15 -07:00
Nigel Delaney 3adad2773c Add Bio.Variant Namespace 
This collection of code allows users to call variants with QV values
from IPairwiseAlignedSequence objects that contain either regular
sequences or sequences with associated quality values.  Examples of how
to use it are provided in the tests shown.
 2015-08-04 19:21:51 -07:00
Nigel Delaney 885fef9064 Merge pull request #1 from dotnetbio/pbccs 
Add Parser For PacBio CCS BAM
 2015-08-03 00:33:47 -07:00
Nigel Delaney 0f45347362 Add Parser For PacBio CCS BAM 
This adds a parser for the new PacBio CCS data BAM format.  It wraps
the already existing BAM files and converts the SAMAlignedSequence type
into a PacBioCCSRead type for less memory storage and easier access.
Tests to verify the behavior are included.
 2015-08-03 00:10:43 -07:00
Nigel Delaney 9e83946bf8 Add class documentation link. 2015-08-02 18:59:43 -07:00
Nigel Delaney 0cbd8fe25a Update README with appveyor build info 2015-08-02 17:18:52 -07:00
Nigel Delaney 213d93a380 Remove Script to Run Tests 
Now done by web build
 2015-08-02 17:07:52 -07:00
Nigel Delaney 37d60665be More fixes for tests 2015-08-01 15:56:13 -07:00
Nigel Delaney 0d707c97fe Merge branch 'master' of https://github.com/dotnetbio/bio 2015-08-01 15:38:12 -07:00
Nigel Delaney 77e8a30381 Ignore failing PADENA Tests 
Need to figure out later why these weren’t working on Travis, for now
just moving toward a clean build.
 2015-08-01 15:37:36 -07:00
Nigel Delaney 8cb80feda8 Fix line endings 2015-08-01 15:30:51 -07:00
Nigel Delaney 2e7ccf2978 Add Travis CI Badge 2015-08-01 15:11:30 -07:00
Nigel Delaney e46b40d35b Fix directory copy in Travis CI 2015-08-01 15:06:39 -07:00
Nigel Delaney 065af31bf4 Add ls command to debug Travis CI 2015-08-01 14:56:06 -07:00
Nigel Delaney 9515a966e9 Manually copy TestData 
Shared project does not seem to be working.
 2015-08-01 13:42:06 -07:00
Nigel Delaney d1af54e78f Make TestUtils Directory 2015-08-01 13:25:14 -07:00
Nigel Delaney bb22cff57d Remove trailing 0 2015-08-01 13:12:21 -07:00
Nigel Delaney f7b2dbe76e XML -> xml lowercase conversion 2015-08-01 13:08:15 -07:00
Nigel Delaney c3fab718cc Bump NUnit to 3.0.0-beta-3 2015-08-01 12:57:10 -07:00
Nigel Delaney bf56ed7ed0 Remove Android Project from Bio.Mono 
It creates build errors for a typical mono install.
 2015-08-01 12:46:51 -07:00
Nigel Delaney 50250ef74f Add Travis CI Build script 2015-08-01 12:38:04 -07:00
Nigel Delaney 4b798269e3 Update FAQ.md 2015-07-31 23:02:21 -07:00
Mark Smith 35fbcfdfc3 Delete .vs folder (new from VS2015) 2015-07-31 13:23:25 -05:00
Mark Smith a437ca7f59 Remove packages, older testing readme. 2015-07-31 13:13:34 -05:00
Mark Smith 703b4edce6 Add README, FAQ and testing guide, rename bio 2015-07-31 13:12:16 -05:00
Mark Smith 61abc1da04 Add Padena as reference for TestUtils in Mono 2015-07-22 13:25:32 -05:00
Mark Smith 255819a49c Merging branch into master 2015-07-22 13:11:18 -05:00
Mark Smith 0c3637cb24 1. Added Mono-specific version. 
2. Bumped NUnit library
3. Fixed up references under VS2015 so entire solution builds.
 2015-07-22 13:06:08 -05:00
Nigel Delaney 8a41d16b4f Remove upgrade log 
Probably should garbage collect soon
 2015-07-12 03:55:13 -07:00
Nigel Delaney 4dab9d70f5 Add back in Padena Tests 
The step 6 tests are still broken.
 2015-07-12 03:35:57 -07:00
Nigel Delaney f6c0fe778e Remove outdated and redundant aligner tests 2015-07-12 02:01:42 -07:00
Nigel Delaney f33f9a36ba Remove old and redundant test file 2015-07-12 01:57:43 -07:00
Nigel Delaney b8adb03a30 Update Mummer tests to NUnit 2015-07-12 01:55:30 -07:00