GenBankFormatter close writer if Open(StreamWriter outStream)

outStream can not be used after Write(ICollection<ISequence> sequences), since it is finally { if (writer != null) { writer.Close(); writer.Dispose(); } } is actua...

Id #9304 | Release: None | Updated: Jun 27, 2015 at 9:03 PM by evolvedmicrobe | Created: Apr 1, 2015 at 1:43 PM by gchen50

Bio.Padena Redundant Path Purger requires equal length paths

In a graph, if two paths go: A->B->C A->D->E->C They are not considered redundant as the redundant path purger requires the paths to be of equal length.

Id #9302 | Release: None | Updated: Jul 14, 2014 at 2:54 PM by sjmercer | Created: Jun 30, 2014 at 9:57 PM by evolvedmicrobe

.NET Bio VS project template not installed for VS2010 or VS2013

As of v1.1, the .NET Bio Console Application project template becomes available in VS2012 but not VS2010 or Vs2013.

Id #9269 | Release: None | Updated: Mar 25, 2014 at 3:54 AM by lbuckingham | Created: Mar 25, 2014 at 3:40 AM by lbuckingham

BAMParser does not check for or write EOF marker

BAM Files now typically now come with a special set of bytes to mark the end of the file. We should update the program to both read and write these bytes to help with data/file validation. See he...

Id #9209 | Release: None | Updated: Feb 9, 2014 at 12:17 AM by evolvedmicrobe | Created: Feb 9, 2014 at 12:17 AM by evolvedmicrobe

Base alphabet inference goof ups

If attempting to load a multiple sequence alignment in FASTA format, if the first species has all gaps on the first line: ""----------------------------------------------------------------------" ...

Id #9020 | Release: None | Updated: Sep 19, 2013 at 1:03 PM by markjulmar | Created: Sep 17, 2013 at 9:20 PM by evolvedmicrobe

Need unit test coverage of MUMmer and NUCmer tools

We need specific unit tests which compare the output against the original http://mummer.sourceforge.net/ implementation. Our output format deviates from the published specification and as a result...

Id #8950 | Release: None | Updated: Aug 15, 2013 at 5:11 PM by evolvedmicrobe | Created: Aug 15, 2013 at 3:30 PM by markjulmar

Section of NUCmer code seems nonsensical

In our ExtendClusters method in NUCmer.cs we do an assignment of the last item in a list before sorting it: Cluster targetCluster = synteny.Clusters.Last(); IList<Cluster> clusters = synteny.Clu...

Id #8949 | Release: None | Updated: Aug 18, 2013 at 1:50 PM by evolvedmicrobe | Created: Aug 15, 2013 at 3:33 AM by evolvedmicrobe

PADENAUtil.exe fails when not run in a console

When not run in a console but from a python script or something, the FastAFormatter bit of code: formatter.MaxSymbolsAllowedPerLine = Math.Min(80, Console.WindowWidth - 2); Decides that it will ou...

Id #8904 | Release: None | Updated: Jul 25, 2013 at 7:47 PM by evolvedmicrobe | Created: Jul 25, 2013 at 7:15 PM by evolvedmicrobe

MapReadsToContigs Tests Fail

Several tests in PADENA are written to assume the direction that an assembled sequence will be output. Whether or not the forward or reverse complement of a sequence is returned after assembly sho...

Id #8849 | Release: None | Updated: Jun 30, 2013 at 8:58 PM by evolvedmicrobe | Created: Jun 30, 2013 at 8:58 PM by evolvedmicrobe

PADENA continues to allow even length k-mers

Even length k-mers create a number of problems, currently the code base allows them both in the input and the tests, leading to unpredictable behavior.

Id #8847 | Release: None | Updated: Jul 1, 2013 at 3:01 AM by evolvedmicrobe | Created: Jun 30, 2013 at 8:10 PM by evolvedmicrobe