User: John Marshall
John Marshall • 1.4k
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- Location:
- Glasgow, Scotland
- Twitter:
- jomarnz
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- 7 minutes ago
- Joined:
- 6 years, 11 months ago
- Email:
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Posts by John Marshall
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Comment:
C: Review of the CIGAR string format
... `=` and `X` appeared in SAM v1.3 in July 2009, in and the surrounding thread. ...
written 5 weeks ago by
John Marshall • 1.4k
0
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3
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195
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... Sadly this text entry box is too narrow for unfortunate contigs named via UUIDs. See PR [samtools/samtools#968](https://github.com/samtools/samtools/pull/968).
In the meantime, there is a workaround to jump to the position you're after using a vanilla samtools tview build: the goto command accepts ...
written 6 weeks ago by
John Marshall • 1.4k
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1
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225
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... > Warning: XSCORE_PARAMETER is not set ... use default setting
That's because that variable is indeed not set *in the environment*.
The shell equivalent of C-shell's `setenv` is `export`, so you need
export XTOOL_PARAMETER=$XTOOL_HOME/parameter
# etc ...
written 6 weeks ago by
John Marshall • 1.4k
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... HTSlib's headers are set up so that they are in an *htslib/* subdirectory of an includedir and used with `#include "htslib/sam.h"` etc. This avoids collisions with other libraries that might provide unrelated headers coincidentally named *sam.h*.
So if your `find` command shows */path/to/the/direct ...
written 6 weeks ago by
John Marshall • 1.4k
6
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... You are moving from building existing packaged tools, which is (admittedly less than ideally) something that many bioinformaticians need to do when they'd really like to be just using the tools, to writing the build infrastructure from scratch for your own tools, which is a software development task ...
written 7 weeks ago by
John Marshall • 1.4k
0
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2
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208
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... > But I am using cython.
Who knew? You said in your question tags that you were using C and/or C++…
If you are using Python and are overly concerned about external dependencies, you might look at the pure Python techniques used in BAMnostic: see . ...
written 7 weeks ago by
John Marshall • 1.4k
• updated
7 weeks ago by
Pierre Lindenbaum ♦ 115k
5
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2
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208
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... BAM files are binary structs compressed in a gzip-compatible way. For non-random streaming read access, if you are willing to use the system zlib library to handle the decompression, it is pretty simple to decode BAM records read via `gzread()` in your own C or C++ code. Refer to the SAM/BAM specifi ...
written 7 weeks ago by
John Marshall • 1.4k
3
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2
answers
208
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2
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... The HTSlib maintainers would love it if you did not do that, as it's just one more place where in future people will be stuck with an outdated version of HTSlib. At least provide configure or make options to use an already-installed HTSlib. ...
written 7 weeks ago by
John Marshall • 1.4k
0
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1
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225
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1
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... Please confirm whether you are using `bedtools intersect -sorted`. ...
written 8 weeks ago by
John Marshall • 1.4k
0
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1
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176
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1
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... Depending on where your bcftools package came from (check with `dpkg -L bcftools`), I think you will find that the existing plugins are in */usr/lib/x86_64-linux-gnu/bcftools/* rather than */usr/local/bcftools/plugins/*.
You need to compile the new plugin *in the context of the BCFtools source code ...
written 8 weeks ago by
John Marshall • 1.4k
Latest awards to John Marshall
Good Answer
7 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Tool for random access to indexed BAM files in S3?
Appreciated
7 weeks ago,
created a post with more than 5 votes.
For A: Tool for random access to indexed BAM files in S3?
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: SAMtools-1.2 sort options documentation
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Appreciated
7 weeks ago,
created a post with more than 5 votes.
For A: Tool for random access to indexed BAM files in S3?
Commentator
7 weeks ago,
created a comment with at least 3 up-votes.
For C: SAM file: same reads ID, slightly different sequence
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Teacher
10 weeks ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Scholar
10 weeks ago,
created an answer that has been accepted.
For A: SAMtools-1.2 sort options documentation
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Guru
18 months ago,
received more than 100 upvotes.
Scholar
19 months ago,
created an answer that has been accepted.
For A: Velvet-SC installation/compilation issues
Good Answer
22 months ago,
created an answer that was upvoted at least 5 times.
For A: Question about sam flags.
Scholar
24 months ago,
created an answer that has been accepted.
For A: Velvet-SC installation/compilation issues
Scholar
2.0 years ago,
created an answer that has been accepted.
For A: Velvet-SC installation/compilation issues
Commentator
2.0 years ago,
created a comment with at least 3 up-votes.
For C: SAM file: same reads ID, slightly different sequence
Good Answer
2.1 years ago,
created an answer that was upvoted at least 5 times.
For A: Question about sam flags.
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