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Forum: Bioinformatics 06-07-2018, 12:09 AM
Replies: 4
Views: 486
Posted By jkbonfield
If you don't have an index or have *many*...

If you don't have an index or have *many* regions, you're probably better off using -T instead of -R which will stream and filter. I have vague recollections though that there may be a difference...
Forum: Bioinformatics 02-02-2018, 07:58 AM
Replies: 1
Views: 1,159
Posted By jkbonfield
Try running ./configure;make first. Does that...

Try running ./configure;make first. Does that work? (Check the output carefully from configure too to see if it works only by dint of removing lzma support entirely!)

If it doesn't, you'll need...
Forum: Bioinformatics 03-28-2017, 01:01 AM
Replies: 12
Views: 1,665
Posted By jkbonfield
I would say the issues wasn't the spaces in the...

I would say the issues wasn't the spaces in the fasta headers but the program that interpreted the headers without any room for the usual ">name comment" syntax. There has never been, as far as I'm...
Forum: Bioinformatics 02-24-2017, 08:15 AM
Replies: 3
Views: 782
Posted By jkbonfield
Not fast, but something like: perl -e...

Not fast, but something like:

perl -e 'while(<>) {if (/^>/) {print;next}; chomp; print $_,"N" x (150-length($_)),"\n"}' in.fasta
Forum: Bioinformatics 11-19-2015, 04:30 AM
Replies: 3
Views: 1,336
Posted By jkbonfield
I've no idea, but you should use samtools-1.2 as...

I've no idea, but you should use samtools-1.2 as 0.1.19 is pretty ancient now.
Forum: Oxford Nanopore 11-06-2015, 12:18 AM
Replies: 15
Views: 5,271
Posted By jkbonfield
In that case, it makes it possible to be more...

In that case, it makes it possible to be more accurate than just guessing based on the random distribution, albeit perhaps also (too?) complex to tease out all the correlations.

Either way, I'm...
Forum: Oxford Nanopore 11-05-2015, 05:05 AM
Replies: 15
Views: 5,271
Posted By jkbonfield
Consensus improvement isn't the same as per-base...

Consensus improvement isn't the same as per-base improvement. I wonder what the difference is there.

Also Jared said it was mainly down to improvements in homopolymers or whether it is simply due...
Forum: Bioinformatics 03-09-2015, 07:09 AM
Replies: 78
Views: 41,216
Posted By jkbonfield
Do the other dialogues work for you, for example...

Do the other dialogues work for you, for example Find Internal Joins? I haven't see cases before where you cannot type into a dialogue box. Which window manager are you using? Is this a genuine...
Forum: Bioinformatics 10-24-2014, 12:48 PM
Replies: 41
Views: 14,522
Posted By jkbonfield
You will of course get output.bam.bam. Oh how I...

You will of course get output.bam.bam. Oh how I hate thee Samtools!
Forum: Bioinformatics 10-23-2014, 04:56 AM
Replies: 78
Views: 41,216
Posted By jkbonfield
I hardly ever run Windows locally so I'm afraid I...

I hardly ever run Windows locally so I'm afraid I don't tend to spot things like this, although we did test it I'm sure.

plotchart is part of "tklib"...
Forum: Bioinformatics 10-13-2014, 04:39 AM
Replies: 8
Views: 1,777
Posted By jkbonfield
There is a compare_sam (not bam, but that's a...

There is a compare_sam (not bam, but that's a trivial conversion) script in the htslib test harness.

https://github.com/samtools/htslib/blob/develop/test/compare_sam.pl

It's pretty crufty and...
Forum: Bioinformatics 02-21-2014, 08:44 AM
Replies: 8
Views: 1,454
Posted By jkbonfield
Perhaps one solution is to compute it in sections...

Perhaps one solution is to compute it in sections (say 1000 reads at a time), computing a vector of ACGT- at each point along with confidences, and then combining those vectors together in a second...
Forum: Bioinformatics 11-08-2013, 12:34 AM
Replies: 4
Views: 2,474
Posted By jkbonfield
Those look to me to be reads that are spanning...

Those look to me to be reads that are spanning two contigs. I assume you either have variable length reads or you're using the Y-Spread function to spread them out a bit (it helps a lot to see...
Forum: Bioinformatics 11-07-2013, 04:48 AM
Replies: 4
Views: 2,474
Posted By jkbonfield
The manual is in a desperate need of an overhaul!...

The manual is in a desperate need of an overhaul!

The colours you are seeing are at the top of the template display, where the single-ended reads or contig spanning read-pairs sit? If so they are...
Forum: Bioinformatics 09-24-2013, 05:10 AM
Replies: 26
Views: 13,368
Posted By jkbonfield
Not that I want to defend CLC, and I've no idea...

Not that I want to defend CLC, and I've no idea precisely why they do this either, but I am also guilty of using my own internal format for Gap5 requiring a full import. Why? Because BAM isn't a...
Forum: Bioinformatics 09-09-2013, 07:48 AM
Replies: 41
Views: 14,522
Posted By jkbonfield
This task is a related one to the bamtofastq...

This task is a related one to the bamtofastq conversion in that collation by name is necessary, but not necessarily a full sort.

Collation is often fast, while sorting is very slow. I don't know...
Forum: Bioinformatics 06-27-2013, 12:52 AM
Replies: 6
Views: 2,864
Posted By jkbonfield
It's not samtools, but maybe still of interest. ...

It's not samtools, but maybe still of interest. I released the new version of Staden Package's io_lib (aka libstaden-read in some linux distribution) which contains a multi-threaded BAM/CRAM/SAM...
Forum: Bioinformatics 06-24-2013, 04:32 AM
Replies: 6
Views: 2,864
Posted By jkbonfield
Not that I know of. I believe the first thing...

Not that I know of. I believe the first thing planned is a new official release of the reorganised code base, so some unknown length of time after that for threading investigations.

We also plan...
Forum: Bioinformatics 06-24-2013, 12:44 AM
Replies: 6
Views: 2,864
Posted By jkbonfield
There are at least two different multi-threading...

There are at least two different multi-threading implementations in Samtools. Heng Li's and Nils Homer's. The latter appears to be more efficient as it multi-threads decoding too, but it's less clear...
Forum: General 05-15-2013, 12:38 AM
Replies: 16
Views: 9,427
Posted By jkbonfield
I forgot to add, CRAM supports random access too....

I forgot to add, CRAM supports random access too. I have a cram_index program to create .crai files and then scramble can use these for random access. On a test I did recently it turned out that...
Forum: General 05-15-2013, 12:33 AM
Replies: 16
Views: 9,427
Posted By jkbonfield
CRAM has both lossy and lossless modes. My own C...

CRAM has both lossy and lossless modes. My own C library currently only supports lossless encoding (but can handle decoding of lossily encoded CRAM files). Vadim's Java provides options for both...
Forum: Bioinformatics 05-13-2013, 04:32 AM
Replies: 4
Views: 1,944
Posted By jkbonfield
I can do it via a truely tortuous route, and...

I can do it via a truely tortuous route, and probably not one you'd want.

Gap5 can import/export both formats, so it can be used as a conversion tool. But it's slow as it builds its own internal...
Forum: Bioinformatics 04-25-2013, 12:19 AM
Replies: 34
Views: 11,860
Posted By jkbonfield
Biobambam (https://github.com/gt1/biobambam) also...

Biobambam (https://github.com/gt1/biobambam) also includes a bamtofastq program. I don't know about speed, but I believe it keeps a hash of recent sequences to allow output of paired end data and...
Forum: General 02-04-2013, 12:38 AM
Replies: 16
Views: 9,427
Posted By jkbonfield
I just noticed this thread, rather late. ...

I just noticed this thread, rather late.

There is CRAM from EBI, which has long term support and handles random access. It's the most direct competitor to BAM I would guess.

Alternatives are...
Forum: Bioinformatics 11-30-2012, 08:15 AM
Replies: 3
Views: 3,350
Posted By jkbonfield
You should be able to export a region of a single...

You should be able to export a region of a single contig as SAM or BAM, and then rerun tg_index on that SAM file to create a new assembly or append (tg_index -a -n) to an existing one.

Precisely...
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