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 10:03 PM by evolvedmicrobe | Created: Apr 1, 2015 at 2:43 PM by gchen50
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 3:54 PM by sjmercer | Created: Jun 30, 2014 at 10:57 PM by evolvedmicrobe
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 4:54 AM by lbuckingham | Created: Mar 25, 2014 at 4:40 AM by lbuckingham
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 1:17 AM by evolvedmicrobe | Created: Feb 9, 2014 at 1:17 AM by evolvedmicrobe
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 2:03 PM by markjulmar | Created: Sep 17, 2013 at 10:20 PM by evolvedmicrobe
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 6:11 PM by evolvedmicrobe | Created: Aug 15, 2013 at 4:30 PM by markjulmar
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 2:50 PM by evolvedmicrobe | Created: Aug 15, 2013 at 4:33 AM by evolvedmicrobe
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 8:47 PM by evolvedmicrobe | Created: Jul 25, 2013 at 8:15 PM by evolvedmicrobe
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 9:58 PM by evolvedmicrobe | Created: Jun 30, 2013 at 9:58 PM by evolvedmicrobe
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 4:01 AM by evolvedmicrobe | Created: Jun 30, 2013 at 9:10 PM by evolvedmicrobe