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I am running `merge-methcounts` to merge the output from `methcounts` (which was run for all genomic contexts, i.e. without `-n`). However, I receive the fatal error: "inconsistent context" for all of…
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Hi,
There seems to be a problems with FixMateInformation crashing with
Exception in thread "main" java.lang.NullPointerException
at htsjdk.samtools.SamPairUtil.setMateInformationOnSupplementa…
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Something I asked about multiple times. Is it true that the T/C wildcards should be happening at the same time as the A/G wildcards? In other words, should the function:
static bool
similar_letters_b…
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`comethylation.` uses `read.alen` to infer read length. This may give odd results for soft-clipped reads or reads containing indels. I need to investigate which of the length methods is most appropria…
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Testing the installer with the new merged versions of UR, workflow, and gms-core.
Getting the following error during metadata import:
```
DBD::Pg::st execute failed: ERROR: column fragment_library…
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seeing these in the logs
example query, {u'doi': [u'10.12688/f1000research.2-217.v1']}
Due to a debug log line where I'm logging the result coming back from crossref. Not a good idea to have things …
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Hi,
I got an exception when running following command:
``` bash
$ java -cp cramtools-2.1.jar net.sf.picard.sam.ValidateSamFile
```
```
Exception in thread "main" java.lang.NoClassDefFoundError: net/…
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Rather than just output these to `STDOUT`, create a file of the `QNAME` and the reason a read was filtered out during QC steps. Add the option to not create this file which instead would direct this o…
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---
Author Name: **Eleni Castro** (@posixeleni)
Original Redmine Issue: 3900, https://redmine.hmdc.harvard.edu/issues/3900
Original Date: 2014-04-29
Original Assignee: Kevin Condon
---
Updated the …
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I've just processed a file with RUM (version: 1.11 Released March 5, 2012), and was trying to sort the resulting SAM file. However, I'm getting an error (reproduced with the line responsible and with …