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Welcome to biogo-user, a general discussion list for the bíogo bioinformatics toolkit for the Go language.

Your question may have been answered already. Before asking, please search the group archive.

Note: This group is moderated. If you are a first-time poster it may take a few hours for your post to appear in the group. If you get a notice that you have been banned (and you're not a spammer) please email dan.kortschak@adelaide.edu.au

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Jack Langberg, Dan Kortschak2

9/26/24

Heterozygous Alleles

On Thu, 2024-09-26 at 07:09 -0700, Jack Langberg wrote: > Is there functionality in biogo to find

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Heterozygous Alleles

On Thu, 2024-09-26 at 07:09 -0700, Jack Langberg wrote: > Is there functionality in biogo to find

9/26/24

Juan Monroy-Nieto, Dan Kortschak2

7/3/24

HTS: What is the correct way to access the sequence of a softclipped alignment?

On Tue, 2024-07-02 at 22:42 -0700, Juan Monroy-Nieto wrote: > When an alignment is soft-clipped,

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HTS: What is the correct way to access the sequence of a softclipped alignment?

On Tue, 2024-07-02 at 22:42 -0700, Juan Monroy-Nieto wrote: > When an alignment is soft-clipped,

7/3/24

서인석, Dan Kortschak2

7/12/22

What is "panic("index: unexpected alignment length")"

On Mon, 2022-07-11 at 21:55 -0700, 서인석 wrote: > What is wrong??? > > internal/index.go line

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What is "panic("index: unexpected alignment length")"

On Mon, 2022-07-11 at 21:55 -0700, 서인석 wrote: > What is wrong??? > > internal/index.go line

7/12/22

Manolis Maragkakis, Dan Kortschak5

4/28/21

biogo/hts scalability for multiple threads

I see. Thanks for the feedback. On Tuesday, April 27, 2021 at 8:13:36 PM UTC-4 Dan Kortschak wrote:

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biogo/hts scalability for multiple threads

I see. Thanks for the feedback. On Tuesday, April 27, 2021 at 8:13:36 PM UTC-4 Dan Kortschak wrote:

4/28/21

Manolis Maragkakis, Dan Kortschak3

7/16/20

When concurrency is enabled, does bam.Reader maintain input record order?

Great. Thanks Dan! On Thursday, July 16, 2020 at 7:00:28 PM UTC-4, Dan Kortschak wrote: It is

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When concurrency is enabled, does bam.Reader maintain input record order?

Great. Thanks Dan! On Thursday, July 16, 2020 at 7:00:28 PM UTC-4, Dan Kortschak wrote: It is

7/16/20

5/28/20

shilling for support

Hi biogo-user and biogo-dev, From the end of June bíogo development will be completely unfunded (it

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shilling for support

Hi biogo-user and biogo-dev, From the end of June bíogo development will be completely unfunded (it

5/28/20

Mic L, Dan Kortschak2

1/23/20

renaming IDs in a GFF3 file

The gff package does not handle GFF3 at this point. On Thu, 2020-01-23 at 00:23 -0800, Mic L wrote:

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renaming IDs in a GFF3 file

The gff package does not handle GFF3 at this point. On Thu, 2020-01-23 at 00:23 -0800, Mic L wrote:

1/23/20

Sebastien Binet, Dan Kortschak3

9/14/18

migrating example to biogo

On Fri, Sep 14, 2018 at 12:16 AM Dan Kortschak <dan.ko...@adelaide.edu.au> wrote: Hi, You

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migrating example to biogo

On Fri, Sep 14, 2018 at 12:16 AM Dan Kortschak <dan.ko...@adelaide.edu.au> wrote: Hi, You

9/14/18

Shawn Rynearson, Dan Kortschak4

1/24/18

Creating ubams from fastq files.

All the sequence types I provide satisfy that interface. In your case, a linear.QSeq would be most

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Creating ubams from fastq files.

All the sequence types I provide satisfy that interface. In your case, a linear.QSeq would be most

1/24/18

Will Rowe, Dan Kortschak5

11/25/17

RNAME changes to UNMAPPED when writing to BAM instead of SAM

Thanks for the explanation - I understand now. Thanks again for taking the time to help me out. Will

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RNAME changes to UNMAPPED when writing to BAM instead of SAM

Thanks for the explanation - I understand now. Thanks again for taking the time to help me out. Will

11/25/17

ay...@grailbio.com, Dan Kortschak6

9/19/17

How to write a .bai file alongside a .bam file ?

One possible solution is to use a single threaded BGZF writer. This exists at 28b030[1]. The code

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How to write a .bai file alongside a .bam file ?

One possible solution is to use a single threaded BGZF writer. This exists at 28b030[1]. The code

9/19/17

ay...@grailbio.com, Dan Kortschak2

9/19/17

Return value of sam.Record.End()

All of the biogo code uses zero-based half-open indexing. Unfortunately many file formats (including

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Return value of sam.Record.End()

All of the biogo code uses zero-based half-open indexing. Unfortunately many file formats (including

9/19/17

Brent Pedersen, Dan Kortschak17

9/19/17

access to Linear index for bam

Just wanted to follow up and let you know this turned out to be quite useful and is already widely

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access to Linear index for bam

Just wanted to follow up and let you know this turned out to be quite useful and is already widely

9/19/17

ay...@grailbio.com, Dan Kortschak3

7/27/17

Invalid .bam files?

I just filed https://github.com/biogo/hts/issues/101 Thanks for looking into it! - Alex On Monday,

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Invalid .bam files?

I just filed https://github.com/biogo/hts/issues/101 Thanks for looking into it! - Alex On Monday,

7/27/17

Brent Pedersen, Dan Kortschak3

5/8/17

seek to random record in bam file

I'd done this with a tabix/bgzf file before by seeking to a random location, finding the next

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seek to random record in bam file

I'd done this with a tabix/bgzf file before by seeking to a random location, finding the next

5/8/17

aboffin, Dan Kortschak3

5/3/17

Using sequtils.Stitch

Thank you Dan, I had overlooked the definitions of fs and fe! I am able to use Stitch with my test

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Using sequtils.Stitch

Thank you Dan, I had overlooked the definitions of fs and fe! I am able to use Stitch with my test

5/3/17

Brent Pedersen, Dan Kortschak11

2/13/17

interval set operations

Agreed. I made the change. On Mon, Feb 13, 2017 at 3:59 PM, Dan Kortschak <dan.kortschak@adelaide.

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interval set operations

Agreed. I made the change. On Mon, Feb 13, 2017 at 3:59 PM, Dan Kortschak <dan.kortschak@adelaide.

2/13/17

Robert Syme, Dan Kortschak3

12/16/16

Type confusion - how to retrieve alphabet.Letters from alphabet.Slice

Perfect. That makes sense. Thanks Dan! -r On Fri, 16 Dec 2016, 5:59 PM Dan Kortschak <dan.

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Type confusion - how to retrieve alphabet.Letters from alphabet.Slice

Perfect. That makes sense. Thanks Dan! -r On Fri, 16 Dec 2016, 5:59 PM Dan Kortschak <dan.

12/16/16

Brent Pedersen, Dan Kortschak11

11/9/16

On Wed, Nov 9, 2016 at 6:52 PM, Dan Kortschak <dan.ko...@adelaide.edu.au> wrote: > Nice.

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On Wed, Nov 9, 2016 at 6:52 PM, Dan Kortschak <dan.ko...@adelaide.edu.au> wrote: > Nice.

11/9/16

1/5/16

sam header parsing is not spec compliant

During development of hts/sam I made a horrendous and unfortunate error in reading the SAM spec,

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sam header parsing is not spec compliant

During development of hts/sam I made a horrendous and unfortunate error in reading the SAM spec,

1/5/16

Brent Pedersen, Dan Kortschak12

9/4/15

On Fri, 2015-09-04 at 21:30 +0000, Dan Kortschak wrote: > Incredible. I give up. This is https://

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On Fri, 2015-09-04 at 21:30 +0000, Dan Kortschak wrote: > Incredible. I give up. This is https://

9/4/15

Brent Pedersen, Dan Kortschak5

5/14/15

support for reading selected seq from fasta.fai ?

On Wed, 2015-05-13 at 21:03 -0600, Brent Pedersen wrote: > I finally got around to this. For now,

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support for reading selected seq from fasta.fai ?

On Wed, 2015-05-13 at 21:03 -0600, Brent Pedersen wrote: > I finally got around to this. For now,

5/14/15

Brent Pedersen, Dan Kortschak3

5/12/15

bam / boom timings

Hi Dan, in a real use-case (at least for me) I did see some slow down with hts.bam with the Record.

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bam / boom timings

Hi Dan, in a real use-case (at least for me) I did see some slow down with hts.bam with the Record.

5/12/15

Brent Pedersen, Dan Kortschak8

4/25/15

cross-compile changes

yes, that works. thanks so much. On Fri, Apr 24, 2015 at 9:02 PM, Dan Kortschak <dan.kortschak@

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cross-compile changes

yes, that works. thanks so much. On Fri, Apr 24, 2015 at 9:02 PM, Dan Kortschak <dan.kortschak@

4/25/15

Huan Truong, Dan Kortschak4

3/31/15

Fwd: What is the purpose of compEdges and compNodes in biogo.graph/undirected?

On Tue, 2015-03-31 at 20:17 -0500, Huan Truong wrote: > Thanks Dan -- for the quick and very

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Fwd: What is the purpose of compEdges and compNodes in biogo.graph/undirected?

On Tue, 2015-03-31 at 20:17 -0500, Huan Truong wrote: > Thanks Dan -- for the quick and very

3/31/15

3/14/15

biogo moving... again

As people may be aware, googlecode is closing. This means that biogo needs to move. I have started

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biogo moving... again

As people may be aware, googlecode is closing. This means that biogo needs to move. I have started

3/14/15

Vasiliy Tolstov, … Dan Kortschak6

3/9/15

The necessary API for doing this is now present in bgzf.Reader. You can set the Reader to stop at the

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The necessary API for doing this is now present in bgzf.Reader. You can set the Reader to stop at the

3/9/15

mgrant...@gmail.com, Dan Kortschak5

10/10/14

Counting repetitions of a sub-sequence.

Thanks! On Fri, Oct 10, 2014 at 7:22 AM, Dan Kortschak <dan.ko...@adelaide.edu.au> wrote: I

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Counting repetitions of a sub-sequence.

Thanks! On Fri, Oct 10, 2014 at 7:22 AM, Dan Kortschak <dan.ko...@adelaide.edu.au> wrote: I

10/10/14

Spencer Kimball, Dan Kortschak20

10/7/14

Problematic input to interval tree yields incorrect overlaps

On Tue, 2014-10-07 at 21:10 -0400, Spencer Kimball wrote: > The use case that triggered this

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Problematic input to interval tree yields incorrect overlaps

On Tue, 2014-10-07 at 21:10 -0400, Spencer Kimball wrote: > The use case that triggered this

10/7/14

Charles Vejnar, Dan Kortschak4

8/14/14

How to use Payload in interval

On Thu, 2014-08-14 at 18:38 -0700, Charles Vejnar wrote: > Thanks for your great help. I think Go

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How to use Payload in interval

On Thu, 2014-08-14 at 18:38 -0700, Charles Vejnar wrote: > Thanks for your great help. I think Go

8/14/14

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