User: John Marshall

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John Marshall1.4k
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1,450
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Location:
Glasgow, Scotland
Twitter:
jomarnz
Last seen:
7 minutes ago
Joined:
6 years, 11 months ago
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k********@gmail.com

Posts by John Marshall

<prev • 87 results • page 1 of 9 • next >
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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 Marshall1.4k
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Answer: A: How to use samtools tview goto with long reference sequence name
... 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 Marshall1.4k
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Answer: A: Xscore Installation Issue using Bash
... > 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 Marshall1.4k
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Comment: C: Can I read chrom, strand, pos, len from bam files without htslib?
... 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 Marshall1.4k
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Answer: A: Minimal example of using htslib from conda to build a simple c file?
... 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 Marshall1.4k
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Comment: C: Is there a single header file somewhere I can use to read bam?
... > 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 Marshall1.4k • updated 7 weeks ago by Pierre Lindenbaum115k
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Answer: A: Is there a single header file somewhere I can use to read bam?
... 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 Marshall1.4k
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Comment: C: Is there a single header file somewhere I can use to read bam?
... 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 Marshall1.4k
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Comment: C: Bedtools intersect alternatives available
... Please confirm whether you are using `bedtools intersect -sorted`. ...
written 8 weeks ago by John Marshall1.4k
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Comment: C: Install vcf2bed plugin for bcftools
... 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 Marshall1.4k

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?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Scholar 15 months ago, created an answer that has been accepted. For A: Question about sam flags.
Scholar 17 months ago, created an answer that has been accepted. For A: Question about sam flags.
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
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: SAM file: same reads ID, slightly different sequence
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Question about sam flags.
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Question about sam flags.

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