User: tgi.tabbott

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tgi.tabbott220
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Posts by tgi.tabbott

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Problem installing bam-readcount 0.7.4
... That's weird. All of the required boost code should be bundled, requiring no special action. There have been a few posts lately about people trying to install/configure their own versions of boost. If you're trying to install bam-readcount v0.7.4, please try doing so without setting any special opti ...
written 4.4 years ago by tgi.tabbott220
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Answer: A: Build error Breakdancer 1.3.6
... This is fixed in the latest development version of breakdancer. If you're actually trying to build v1.3.6 (by doing git checkout v1.3.6), then set the environment variable CXXFLAGS to -DGTEST_USE_OWN_TR1_TUPLE=1. For bash: git clone ... ... git checkout v1.3.6 export CXXFLAGS=-DGTEST_USE_OWN_TR1 ...
written 4.8 years ago by tgi.tabbott220
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Answer: A: Breakdancer inaccurate output.
... This is due to supplemental alignments on the same sequence as the primary alignment sneaking in and confusing breakdancer. I just pushed a fix to github. If you grab the latest, these CTX on the same sequence calls should go away. ...
written 4.9 years ago by tgi.tabbott220
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Comment: C: Breakdancer Max Kahan Error:0
... Agreed lol. I added that a long time ago when I was worried about numerical precision in the scoring code, and never got around to taking it out... until now. It's gone in master on github :) ...
written 5.1 years ago by tgi.tabbott220
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Answer: A: bam-readcount reports all reference bases as N
... The only way I was able to reproduce this type of problem was by manually changing the reference fasta in a way that invalidates the index. Assuming you have samtools handy, what is the result of: samtools faidx ref.fa NODE_14_length_46_cov_1.239130:50-52 where ref.fa is your reference fasta? If ...
written 5.1 years ago by tgi.tabbott220
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Comment: C: Error Running Breakdancer-Max: Max Kahan Error: 0
... This was in fact a bug. It's been fixed on master and tagged v1.4.4. If you git pull to update your checkout and try again, you may get a better result. ...
written 5.5 years ago by tgi.tabbott220
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Answer: A: Trouble Installing Breakdancer 1.4.2: Boost Libraries Inexplicably Not Visible
... Hello. I just pushed a new version to master that includes the required parts of boost. If you update (git pull) from github, or simply reclone the repository, you should be able to proceed without having to explicitly install boost. ...
written 5.6 years ago by tgi.tabbott220
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Answer: A: Somatic Sniper Compilation Issues
... Hello. Please make sure you export the environment variable SAMTOOLS_ROOT to point to the directory where you compiled samtools. This directory should contain bam.h as well as libbam.a. You may need to remove the contents of your build directory and rerun cmake after doing so as it could be caching ...
written 5.9 years ago by tgi.tabbott220
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Comment: C: 'Floating Point Exception' Error While Running Somaticsniper
... No problem. I guess that newer versions of samtools may have an incompatible .fai format. That is good to know! ...
written 6.0 years ago by tgi.tabbott220
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Answer: A: 'Floating Point Exception' Error While Running Somaticsniper
... I see the error indicated that a core file was dumped. Is that the case, and if so, is it >0bytes in size? If you have a valid core file, then we can try to get stack trace information from it. To do this, assuming you have gdb installed (which should be the case if the "Development Tools" packag ...
written 6.0 years ago by tgi.tabbott220

Latest awards to tgi.tabbott

Appreciated 4.8 years ago, created a post with more than 5 votes. For A: Bam-Readcount: How Is "Average Mismatch Quality Sum" Calculated?
Scholar 4.9 years ago, created an answer that has been accepted. For A: Breakdancer inaccurate output.
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: 'Floating Point Exception' Error While Running Somaticsniper
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Ibwa Optimization
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Bam-Readcount: How Is "Average Mismatch Quality Sum" Calculated?

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