Comments (6)
Yup, it is default with Q 20. Should I change that?
from htstream.
So, the current behavior is:
Find first occurrence of a read, if average Qscore (across all q-scores in both pairs) is >= 20 keep it and skip all future reads, if averageQ is < 20 store it in memory until a read with better q-score is found?
I kind of like it, I think adding more details about the behavior to --help would be a good choice :)
from htstream.
Exactly. If no read with a better q-score is found, it will be written at the end. Should this be the default or user input?
I think the mystery of what software does is invigorating part. :) Nah, you are spot on, once I get the N-Remover merged in and the bugs squashed, I will start writing.
from htstream.
Okay, I'm fine with this behavior as default personally. I'm not sure how @msettles will feel. Certainly documenting it would help.
One request would be to make the "q" setting configurable. For example, perhaps I want to set q=30 as the average for a shorter-read/high quality run.
from htstream.
Okay, it is now configurable with -q option. Default is 40, so only "perfect" reads are written out by default, however, you can set it to whatever you would like.
Since I'm being lazy, it is in the N remover commit so I will close this once it is merged into master.
from htstream.
Cool.
from htstream.
Related Issues (20)
- Feature downgrade actually, remove -a option from SuperD
- -m (minLength) option removed from hts_QWindowTrim, but does not exist in hts_CutTrim HOT 3
- Flag use HOT 1
- Is "percentage-hits" calculated properly for SeqScreener? HOT 1
- SuperDeduper ignoring reads HOT 6
- hts_Primers doesn't seem to read multi-fasta files correctly
- hts_Primers - error message HOT 4
- Version incorrect and CMAKE_PREFIX_PATH not working HOT 5
- How to cite HTStream? :-) HOT 2
- hts_LengthFilter is missing from the documentation!
- citation? HOT 2
- Add to CutTrim, trim to length from 5' or 3'
- pointer error in hts_Stats HOT 1
- Compiling from source fails on Ubuntu 22.04.1 HOT 2
- Remaining adapter sequence
- Order of input files to hts_SeqScreener changes hits reported when R1/R2 lengths differ
- "no such file or directory" error HOT 2
- munmap_chunk(): invalid pointer error HOT 3
- Issue in Common: Memory Leak in `check_open_r` (not closing file) HOT 2
- Mac version available on github, via Brew, and on bioconda is outdated
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from htstream.