User: John Marshall
John Marshall • 1.1k
- Reputation:
- 1,110
- Status:
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- Location:
- Glasgow, Scotland
- Twitter:
- jomarnz
- Last seen:
- 19 hours ago
- Joined:
- 5 years, 8 months ago
- Email:
- k********@gmail.com
Posts by John Marshall
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3
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1
answer
139
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... The article you're looking at is an ancient web page discussing the old **pileup** format, which is similar to but a simplified version of **mpileup** format, which replaced the old format with the arrival of the `samtools mpileup` command quite some years ago.
Instead you should look at the (admit ...
written 15 days ago by
John Marshall • 1.1k
0
votes
2
answers
182
views
2
answers
Answer:
A: BAM Index Chunks
... `chunk_beg`..`chunk_end` is the range of file offsets within the BAM file telling you where in the file the records are. There can be several chunks because the read records within a bin are not necessarily all contiguous in the BAM file — there can be reads from other bins interspersed with them.
...
written 22 days ago by
John Marshall • 1.1k
1
vote
3
answers
345
views
3
answers
Answer:
A: faidx implementation with C++
... Read , which discusses the format of _.fai_ files and how they are used to index well-formatted FASTA files. Working from this will be clearer than working from the implementation in HTSlib, and when you are more familiar with it the HTSlib/Samtools implementation may make a bit more sense. ...
written 4 weeks ago by
John Marshall • 1.1k
2
votes
2
answers
281
views
2
answers
... There's also text about this in §1.4 talking specifically about SAM's QUAL: “This field can be a ‘*’ when quality is not stored”.
Incidentally, if the text about “a sequence of 0xFF if absent” is on p16 of your copy of the SAM specification, then you have a somewhat out of date specification from b ...
written 4 weeks ago by
John Marshall • 1.1k
1
vote
2
answers
281
views
2
answers
... The BAM “run of 0xFF values” is thus so that the offset within the record to the auxiliary data is the same regardless of QUAL data being present or absent. ...
written 4 weeks ago by
John Marshall • 1.1k
2
votes
1
answer
215
views
1
answers
... The file it's looking for is `ltdl.h`. A web search for "red hat ltdl.h" shows that this will be supplied by the **libtool-ltdl-devel** package, which is a separate subsidiary of the **libtool** package that provides the `/usr/bin/libtool` that is present.
It's possible to install this development ...
written 11 weeks ago by
John Marshall • 1.1k
2
votes
1
answer
192
views
1
answers
... The friendlier URL is http://samtools.github.io/hts-specs/SAMtags.pdf — better to point people to that than to an URL containing details like branch names that may change in future. ...
written 3 months ago by
John Marshall • 1.1k
0
votes
2
answers
232
views
2
answers
... README.md is a different file containing different information that is less relevant here. The INSTALL and README files I referred to are in the release tarballs that Alex will have downloaded and also in the Git source repositories. ...
written 4 months ago by
John Marshall • 1.1k
1
vote
2
answers
232
views
2
answers
... Yes.
You might look at the documentation in the INSTALL files in htslib and samtools, and also at samtools's README. ...
written 4 months ago by
John Marshall • 1.1k
0
votes
1
answer
273
views
1
answers
... For help using this, please post to the samtools-help mailing list. Filing a GitHub issue is more for when you've run into an actual bug, and is less useful for usage problems like this because the conversation will be seen by fewer of your fellow samtools users. ...
written 7 months ago by
John Marshall • 1.1k
Latest awards to John Marshall
Guru
3 months ago,
received more than 100 upvotes.
Scholar
4 months ago,
created an answer that has been accepted.
For A: Velvet-SC installation/compilation issues
Good Answer
7 months ago,
created an answer that was upvoted at least 5 times.
For A: Question about sam flags.
Scholar
9 months ago,
created an answer that has been accepted.
For A: Velvet-SC installation/compilation issues
Scholar
9 months ago,
created an answer that has been accepted.
For A: Velvet-SC installation/compilation issues
Commentator
9 months ago,
created a comment with at least 3 up-votes.
For C: SAM file: same reads ID, slightly different sequence
Good Answer
10 months ago,
created an answer that was upvoted at least 5 times.
For A: Question about sam flags.
Good Answer
22 months ago,
created an answer that was upvoted at least 5 times.
For A: Question about sam flags.
Scholar
23 months 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: Error Calling Samtools View On Bwa Sam Output
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: Velvet-SC installation/compilation issues
Teacher
2.7 years ago,
created an answer with at least 3 up-votes.
For A: Error Calling Samtools View On Bwa Sam Output
Teacher
2.8 years ago,
created an answer with at least 3 up-votes.
For A: Error Calling Samtools View On Bwa Sam Output
Good Answer
2.8 years ago,
created an answer that was upvoted at least 5 times.
For A: Question about sam flags.
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