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Pysam User group

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Feb 13

Apologies for the recent spam

My apologies for the recent spam on the mailing list. We are in the process of preventing further

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Apologies for the recent spam

My apologies for the recent spam on the mailing list. We are in the process of preventing further

Feb 13

11/25/25

using pysam with FFI to htslib-based c/cpp tools

Hello, I have a program written in C/C++ using htslib that generates bam1_t objects. I'd like to

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using pysam with FFI to htslib-based c/cpp tools

Hello, I have a program written in C/C++ using htslib that generates bam1_t objects. I'd like to

11/25/25

6/19/25

[collaboration] Add support for Stranded RNA-seq

Hi, At the moment, Pysam does not support stranded RNA-seq analysis. What I mean is that with

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[collaboration] Add support for Stranded RNA-seq

Hi, At the moment, Pysam does not support stranded RNA-seq analysis. What I mean is that with

6/19/25

J, … teepean474

4/21/24

Installing Pysam....

At the moment pysam works only when compiled with MinGW using MSYS2 shell so it won't be

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Installing Pysam....

At the moment pysam works only when compiled with MinGW using MSYS2 shell so it won't be

4/21/24

Aleksandra Galitsyna, Andreas Heger2

2/16/24

Merging two SAM entries?

Hi Aleksandra, unfortunately there is no direct functionality in pysam. However, SAM are easily

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Merging two SAM entries?

Hi Aleksandra, unfortunately there is no direct functionality in pysam. However, SAM are easily

2/16/24

Gregory Dougherty2

1/4/24

How do I use pysam to read header?

Turns out the answer is: import pysam cram = pysam.AlignmentFile (theCram, 'rc') cramHeader =

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How do I use pysam to read header?

Turns out the answer is: import pysam cram = pysam.AlignmentFile (theCram, 'rc') cramHeader =

1/4/24

12/19/23

Error while installing pysamstats in Oracle VM VirtualBox

Hi, I am getting this error while installing pysamstats in Oracle VM VirtualBox (base) shxyz@shxyz-

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Error while installing pysamstats in Oracle VM VirtualBox

Hi, I am getting this error while installing pysamstats in Oracle VM VirtualBox (base) shxyz@shxyz-

12/19/23

9/5/23

Cavity Field Detected.

To whom it may concern I want to investigate small-scale CSP plants using different heliostat field

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Cavity Field Detected.

To whom it may concern I want to investigate small-scale CSP plants using different heliostat field

9/5/23

7/15/23

PileupColumn data

A PileupColumn object provides get_query_names() and get_query_sequences(). Both return lists. Is it

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PileupColumn data

A PileupColumn object provides get_query_names() and get_query_sequences(). Both return lists. Is it

7/15/23

Chloe Saras Thangavelu, Sebastian Luna Valero2

6/13/23

Unable to install pysam with Python 3.8 or 3.10

Hi, I believe the problem is that pysam is only available for Linux/OSX and you are using Windows:

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Unable to install pysam with Python 3.8 or 3.10

Hi, I believe the problem is that pysam is only available for Linux/OSX and you are using Windows:

6/13/23

5/1/23

the secondary alignments were ignored by pysam in my linux platfrom

I'd like to find out the equally best alignments in the bam. I found all the secondary alignments

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the secondary alignments were ignored by pysam in my linux platfrom

I'd like to find out the equally best alignments in the bam. I found all the secondary alignments

5/1/23

3/24/23

Keep IndexedReads built index

Hello everyone, is there any way how we can preserve the index built by IndexedReads? I tried

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Keep IndexedReads built index

Hello everyone, is there any way how we can preserve the index built by IndexedReads? I tried

3/24/23

myourshaw, … Peter Cock4

12/31/22

pip install pysam fails with Python 3.8.0

I'm guessing that means your Linux is too old for manylinux_2_24, which is the glib version. You

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pip install pysam fails with Python 3.8.0

I'm guessing that means your Linux is too old for manylinux_2_24, which is the glib version. You

12/31/22

Andrea Giometto

11/19/22

uninstall compiled Pysam

I need to downgrade from Pysam 0.8.3 to 0.8.2.1. I installed Pysam by compiling it. How can I

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uninstall compiled Pysam

I need to downgrade from Pysam 0.8.3 to 0.8.2.1. I installed Pysam by compiling it. How can I

11/19/22

10/25/22

pysam negative strand coverage counts

Hello, I am using pysam & pysamstats to get the coverage count on each strand, but it seems that

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pysam negative strand coverage counts

Hello, I am using pysam & pysamstats to get the coverage count on each strand, but it seems that

10/25/22

8/31/22

Implementing a custom parser, similar to pysam.asBed()

Hi pysam community, I am aware that pysam is able to read tabix indexed files. For example: for row

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Implementing a custom parser, similar to pysam.asBed()

Hi pysam community, I am aware that pysam is able to read tabix indexed files. For example: for row

8/31/22

Stuart Hay, … teepean474

3/15/22

Windows version of pysam

With the following as a guide it is possible to compile pysam with a recent version of MSYS2/MinGW-

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Windows version of pysam

With the following as a guide it is possible to compile pysam with a recent version of MSYS2/MinGW-

3/15/22

Jia Zheng, Hassan Raza2

3/12/22

pysam 0.16.0.1 and pysam 0.9.1 give different results

Use the latest pysam version, yes there were some updates which corrected and improved the outputs.

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pysam 0.16.0.1 and pysam 0.9.1 give different results

Use the latest pysam version, yes there were some updates which corrected and improved the outputs.

3/12/22

2/28/22

Installation not working ModuleNotFoundError: No module named 'pysamstats.opt'

To note. i think i got something working but i get the following error pysamstats --fasta ~/workdir/

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Installation not working ModuleNotFoundError: No module named 'pysamstats.opt'

To note. i think i got something working but i get the following error pysamstats --fasta ~/workdir/

2/28/22

Tony Lee, … Chrystelle Delord3

2/12/22

Issues with pysam install on an AWS EC2

Dear all, Please allow me to join that thread, as I suspect I might having similar environment

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Issues with pysam install on an AWS EC2

Dear all, Please allow me to join that thread, as I suspect I might having similar environment

2/12/22

12/15/21

Can we seriously not post images or links?

Thats pretty insane for a help community, no?

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Can we seriously not post images or links?

Thats pretty insane for a help community, no?

12/15/21

11/30/21

A more efficient way to do pileup?

Hello, I need to have a pileup for some pre-defined regions for a chromosome. It would be similar to

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A more efficient way to do pileup?

Hello, I need to have a pileup for some pre-defined regions for a chromosome. It would be similar to

11/30/21

Tios, Marcel Martin3

10/21/21

Access to FORMAT values of a vcf record

Thank you so much! 2021년 10월 19일 화요일 오후 4시 46분 6초 UTC+9에 marcel...@scilifelab.se님이 작성: On 19/10/2021

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Access to FORMAT values of a vcf record

Thank you so much! 2021년 10월 19일 화요일 오후 4시 46분 6초 UTC+9에 marcel...@scilifelab.se님이 작성: On 19/10/2021

10/21/21

10/4/21

Pickling AlignedSegment

Hello, I saw that this is an already discussed issue, but I'm also trying to do something with

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Pickling AlignedSegment

Hello, I saw that this is an already discussed issue, but I'm also trying to do something with

10/4/21

Aditya Garg, Marcel Martin2

9/11/21

Pysam installation error through conda on linux env

Hi Adita, On 11/09/2021 01.27, Aditya Garg wrote: > I am trying to install pysam using the

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Pysam installation error through conda on linux env

Hi Adita, On 11/09/2021 01.27, Aditya Garg wrote: > I am trying to install pysam using the

9/11/21

Matthew Cserhati

8/25/21

retrieving fields in vcf file

Hello all, This isn't exactly pysam, but pyvcf-related. Does anyone know how to retrieve the

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retrieving fields in vcf file

Hello all, This isn't exactly pysam, but pyvcf-related. Does anyone know how to retrieve the

8/25/21

Anna Cunningham, Marcel Martin2

8/24/21

Pysam stub files for mypy?

On 2021-08-24 02:29, Anna Cunningham wrote: > I'm trying to find pysam stub files > <

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Pysam stub files for mypy?

On 2021-08-24 02:29, Anna Cunningham wrote: > I'm trying to find pysam stub files > <

8/24/21

7/27/21

Combining VCF files

I've been set the task of combining VCF files from varying callers into one unified VCF. As part

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Combining VCF files

I've been set the task of combining VCF files from varying callers into one unified VCF. As part

7/27/21

Matthew Cserhati, Marcel Martin9

6/14/21

pysam.AlignmentFile not working...

On 14/06/2021 21.12, Matthew Cserhati wrote: > now I get this: > > (env) [mcserhati@

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pysam.AlignmentFile not working...

On 14/06/2021 21.12, Matthew Cserhati wrote: > now I get this: > > (env) [mcserhati@

6/14/21

Endre Bakken Stovner

6/9/21

Problems importing pysam on mac: Library not loaded: @rpath/libctabixproxies.cpython-39-darwin.so

I am having problems importing pysam in this file: https://github.com/biocore-ntnu/epic2/blob/master/

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Problems importing pysam on mac: Library not loaded: @rpath/libctabixproxies.cpython-39-darwin.so

I am having problems importing pysam in this file: https://github.com/biocore-ntnu/epic2/blob/master/

6/9/21

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