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Forum: Open Genomics Engine Project 11-20-2012, 07:53 PM
Replies: 1
Views: 6,999
Posted By leecbaker
Hello Ashreid, We would love to have more...

Hello Ashreid,

We would love to have more people contributing to the codebase.

Getting started, I would first make sure you can:

Clone the source from github and build openge (See the...
Forum: Bioinformatics 10-30-2012, 10:37 AM
Replies: 7
Views: 2,346
Posted By leecbaker
The BAM file came from an unreleased development...

The BAM file came from an unreleased development version of OpenGE (https://github.com/adaptivegenome/openge/). We have been developing faster multithreaded BAM IO code, and evidently still have a...
Forum: Bioinformatics 10-29-2012, 11:48 PM
Replies: 7
Views: 2,346
Posted By leecbaker
Maubp, good idea. I ran the same commands,...

Maubp, good idea. I ran the same commands, gunzip'ed the resulting BAM files, and then compared the binary data inside. The only differences between the working and nonworking files was that the bin...
Forum: Bioinformatics 10-28-2012, 10:03 PM
Replies: 7
Views: 2,346
Posted By leecbaker
Possible samtools view bug

I'm using samtools to extract some regions from a BAM file, and in some situations, I don't get back all of the reads that overlap the region.

For example:
Looking for all reads that overlap the...
Forum: Open Genomics Engine Project 08-30-2012, 08:46 AM
Replies: 1
Views: 8,047
Posted By leecbaker
OpenGE 0.2 Release

We're pleased to announce the release of OpenGE 0.2 .

Major highlights include:
* Local realignment function. This function realigns reads near indels, using all reads in the region around the...
Forum: Bioinformatics 07-25-2012, 08:49 AM
Replies: 63
Views: 34,495
Posted By leecbaker
Hello Richard, Primary developer of OpenGE...

Hello Richard,

Primary developer of OpenGE here. My primary development machine uses CMake 2.8.8 (the latest) with Boost 1.49, and I haven't run into any problems with this version yet. Can you...
Forum: Open Genomics Engine Project 07-03-2012, 11:51 AM
Replies: 5
Views: 8,116
Posted By leecbaker
As we continue to work on more new features, we...

As we continue to work on more new features, we want to let you know that we have added FASTQ as a supported output format, in addition to the SAM and BAM support that we currently have.

Support...
Forum: Open Genomics Engine Project 06-16-2012, 12:52 AM
Replies: 5
Views: 8,116
Posted By leecbaker
OpenGE 0.1.1 released

We're pleased to announce that version 0.1.1 of OpenGE is available for download. This release contains some performance work, minor new features, and bug fixes.

New in this release:
* Mark...
Showing results 1 to 8 of 8

 


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