samtools | C using htslib | Genomics library

by samtools C Version: 1.17 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | samtools Summary

samtools is a C library typically used in Artificial Intelligence, Genomics applications. samtools has no bugs, it has no vulnerabilities and it has medium support. However samtools has a Non-SPDX License. You can download it from GitHub.

See [INSTALL] INSTALL) for complete details. [Release tarballs][download] contain generated files that have not been committed to this repository, so building the code from a Git repository requires extra steps:. By default, this will build against an HTSlib source tree in ../htslib. You can alter this to a source tree elsewhere or to a previously-installed HTSlib by configuring with --with-htslib=DIR.

Support

Quality

Security

License

Reuse

Support

samtools has a medium active ecosystem.

It has 1358 star(s) with 534 fork(s). There are 102 watchers for this library.

It had no major release in the last 12 months.

There are 163 open issues and 933 have been closed. On average issues are closed in 69 days. There are 15 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of samtools is 1.17

Quality

samtools has 0 bugs and 0 code smells.

Security

samtools has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

samtools code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

samtools has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

samtools releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

It has 158 lines of code, 4 functions and 1 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

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samtools Key Features

No Key Features are available at this moment for samtools.

samtools Examples and Code Snippets

No Code Snippets are available at this moment for samtools.

Community Discussions

Trending Discussions on samtools

How to save outputs from current directory to another a directory in a shell script?

using grep (or awk) to extract two consecutive words

Write the outcome of a for loop in multiple files in a single file in shell

My merge overlapping coordinate python script cost too much memory

Keep getting error: [E::fai_build3_core] Failed to open the file --regions for a script I have been using

How to output a value channel that has paths using Nextflow

Using bash how to iterate through lines in a txt file and sequentially pair up every two lines

How to apply for loop in bash terminal

Creating a loop for a function

Dependencies plot-vcfstats in conda environment

QUESTION

How to save outputs from current directory to another a directory in a shell script?

Asked 2022-Mar-24 at 23:55

I want to read all files in my current directory and would like to save the result on another directory. The code is below but could not get the files in the excepted directory. Does anyone can help me.

...

ANSWER

Answered 2022-Mar-24 at 23:55

Here's a fixed version of your code:

Source https://stackoverflow.com/questions/71603106

QUESTION

using grep (or awk) to extract two consecutive words

Asked 2022-Mar-23 at 17:50

I have a BAM file from which I need to extract the two words starting with "PL:Z...", followed by "PR:Z..."

I started trying with the first word, but no luck :

...

ANSWER

Answered 2022-Mar-16 at 15:19

You may use this awk that loops through all the fields and matches a field using regular expression ^P[LR]:Z: and appends it into a variable to print it in the end.

Source https://stackoverflow.com/questions/71499501

QUESTION

Write the outcome of a for loop in multiple files in a single file in shell

Asked 2022-Mar-19 at 22:28

I am new to shell scripting (bash/awk...etc) so please excuse me for my stupid question. I am aware that to many of you this is so easy

I have multiple files that look like this:

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ANSWER

Answered 2022-Mar-19 at 21:53

I suggest with bash:

Source https://stackoverflow.com/questions/71542259

QUESTION

My merge overlapping coordinate python script cost too much memory

Asked 2022-Mar-15 at 01:12

I'm trying to choose unique regions for my Non-invasive Prenatal Testing (NIPT) project. I have done following steps:

Create an artificial fasta file contains 50bp sequence. On each chromosome, the next sequence overlap 40bp from previous sequence
Align and only chosen no mismatch sequence

I have a .sam file about 40gb, on the next step I try to merge all overlapping coordinates to one .bed file for using in samtools. This is my python script to do that:

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ANSWER

Answered 2022-Mar-14 at 04:13

Hopefully this does the trick. Hard to know since I'm working without having the input file or knowing what the output should look like and can't really run the code to check for errors, but here's what I've tried to do:

Eliminate raw and go straight to creating treat1; and
Eliminate treat2 and go straight to writing to bedfile. I opened bedfile right off the bat and everything in your program is done with that file open.

If this does what you need but still crashes, then perhaps you can read through each file twice to get last_coord at the end of the treat1 and then read through it again to "recreate" each line of treat1 individually and apply it to defining what needs to be written into the file.

Without really knowing the details of what you're doing (I do not work anywhere close to a field that would apply samtools).

Source https://stackoverflow.com/questions/71462634

QUESTION

Keep getting error: [E::fai_build3_core] Failed to open the file --regions for a script I have been using

Asked 2022-Feb-25 at 19:45

I have been using the below script however, I keep getting an error on the output. Any ideas why?

...

ANSWER

Answered 2022-Feb-25 at 19:45

Suggesting to replace line:

Source https://stackoverflow.com/questions/71266991

QUESTION

How to output a value channel that has paths using Nextflow

Asked 2022-Jan-21 at 03:06

Say one has some process that outputs files (e.g., converting sam to bam files) and one wants the output of the process to be a value channel so that it can be reused many times. Can one do this during the output of the channel? Or, does one have to call an operator (first?) on the queue channel after it has been output and that process completed?

Here is an example:

...

ANSWER

Answered 2022-Jan-21 at 03:06

Ultimately this depends on if the 'alignments' channel is already a value channel or not:

A value channel is implicitly created by a process when an input specifies a simple value in the from clause. Moreover, a value channel is also implicitly created as output for a process whose inputs are only value channels.

Note that this will create a queue channel:

Source https://stackoverflow.com/questions/70790676

QUESTION

Using bash how to iterate through lines in a txt file and sequentially pair up every two lines

Asked 2022-Jan-20 at 14:56

Hi I am attempting to use bash to iterate through a .txt file which contains the following lines. This is a smaller subset of the full list of fastq files, but all samples follow the same patterns.

...

ANSWER

Answered 2022-Jan-20 at 14:56

Why not reading 2 lines at a time? Remove echo before bwa... when you'll be satisfied with the result.

Source https://stackoverflow.com/questions/70785317

QUESTION

How to apply for loop in bash terminal

Asked 2021-Nov-16 at 11:14

I am new to bash and would like to get help how to run for loop.

Here is my question, I have 10 different sorted bam files(*.sorted.bam) and I would like to do indexing for each sorted bam files.

I know how to run it for single file using the command below

...

ANSWER

Answered 2021-Nov-16 at 11:14

you can use the for..in loop like this:

Source https://stackoverflow.com/questions/69987838

QUESTION

Creating a loop for a function

Asked 2021-Nov-08 at 18:16

I've essentially created a function which inputs a string, and then adds the integers which appear before each unique letter. (e.g. 21M4D35M, would provide 56M and 4D).

...

ANSWER

Answered 2021-Nov-08 at 18:16

An efficient solution would be to used collections.Counter:

Source https://stackoverflow.com/questions/69887868

QUESTION

Dependencies plot-vcfstats in conda environment

Asked 2021-Oct-22 at 04:24

I have a conda environment where I have packages including bcftools installed. I am using bcftools stats to generate some stats on my VCF files. Then, I want to plot the generated stats using plot-vcfstats, also from bcftools. However, this command turned out to be dependent on certain packages that didn't install when I installed bcftools in my conda env. The output I got when running plot-vcfstats:

...

ANSWER

Answered 2021-Oct-22 at 04:24

Seems like a mess. Some of the comments in this open issue imply that Conda's texlive-core is broken, but not really clear there is an authoritative response there.

On osx-64 platform, I can get semi-functionality with the environment:

Source https://stackoverflow.com/questions/69659849

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install samtools

You can download it from GitHub.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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