User: John Marshall

gravatar for John Marshall
John Marshall1.5k
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1,470
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Location:
Glasgow, Scotland
Twitter:
jomarnz
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an hour ago
Joined:
7 years, 1 month ago
Email:
k********@gmail.com

Posts by John Marshall

<prev • 90 results • page 1 of 9 • next >
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Answer: A: samtools " Assertion `iter->curr_off == iter->off[iter->i].v' failed". "
... That error message indicates that you are using samtools 0.1.19. This was released almost six years ago, and still using it is a problem in itself… ...
written 8 days ago by John Marshall1.5k
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Comment: C: install Primer3 on Ubuntu
... Do you conda advocates ever get bored of saying “have you tried conda?”? What would be useful would be if you said “This works in bioconda because we have invented an unofficial 2.4.1a release that includes a few post-2.4.0 commits from upstream primer3, notably a fix for this *thal.c:429* problem. ...
written 5 weeks ago by John Marshall1.5k
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Comment: C: install Primer3 on Ubuntu
... This worked because you are now building git HEAD rather than the 2.4.0 release. The *thal.c:429* et al errors in the original question were bugs that were fixed in [May 2018](https://github.com/primer3-org/primer3/commit/2a04aa2e11e3c7a7d91c208b842a76754a840c87#diff-f8db35be2213e9f267cb700f904a89b7 ...
written 5 weeks ago by John Marshall1.5k
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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 3 months ago by John Marshall1.5k
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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 3 months ago by John Marshall1.5k
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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 3 months ago by John Marshall1.5k
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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 4 months ago by John Marshall1.5k
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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 4 months ago by John Marshall1.5k
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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 4 months ago by John Marshall1.5k • updated 4 months ago by Pierre Lindenbaum117k
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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 4 months ago by John Marshall1.5k

Latest awards to John Marshall

Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Tool for random access to indexed BAM files in S3?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Tool for random access to indexed BAM files in S3?
Scholar 4 months ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Tool for random access to indexed BAM files in S3?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: SAM file: same reads ID, slightly different sequence
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Scholar 4 months ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Scholar 17 months ago, created an answer that has been accepted. For A: Question about sam flags.
Scholar 20 months ago, created an answer that has been accepted. For A: Question about sam flags.
Guru 20 months ago, received more than 100 upvotes.
Scholar 21 months ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Good Answer 2.0 years ago, created an answer that was upvoted at least 5 times. For A: Question about sam flags.
Scholar 2.2 years ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Scholar 2.2 years ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: SAM file: same reads ID, slightly different sequence
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: Question about sam flags.
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: Question about sam flags.

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