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License: GNU General Public License v3.0
FastQC port to Qt5: A quality control tool for high throughput sequence data.
License: GNU General Public License v3.0
Drop file doesn't work with extension containing dot.
For exemple : mytest.sample.fastq.gz cannot be dropped
I run fastqt on this file : test.fastq.zip
After a little bit of investigation, with gdb I found fastqt crash on lengthdistributionanalysis.cpp line 118.
Use Quazip
Exporting graph each graph as png .
Exporting all analyse as pdf
Try to run fastqt on windows.
You need to compile KArchive first. Then create a win32/ folder and put the library inside.
See :
https://github.com/labsquare/CuteVCF/tree/master/win32
https://github.com/labsquare/CuteVCF/blob/master/CuteVcf.pro#L29
Change color or icon layout .. It's ugly actually, almost for windows
See @ikit advice
I have to close the windows to do anything else.
During counting reads number, There is no information.. And times doesn't run.
Open a Huge fastq.bz2 . It keeps 0 percent without showing anything.
Reading gz file, means random access and not sequencial access.
So, actually, I cannot compute the percent progress with the following line :
file.pos() / file.size()
https://github.com/labsquare/fastQt/blob/master/sequence/abstractsequencereader.cpp#L37
Need to find a solution ... @Arkanosis any idea ?
Drop fastq file from FS to the main view keep analysis at 0 %/
Actualy we use the last extension in filename to choose the compression format, we can replace it by read the magic number.
For check if file is fastq just read the first character of first 4 lines -> @, [a-Z], +, [.]
All in the title !
Quote from @Arkanosis :
I'll rewrite this to avoid decompressing files twice (I'm pretty sure more time is spent currently decompressing compared to actually computing the statistics). Feel free to clean up, though, as I'm not sure when I'll do this.
If you want this functionality is implement please add comment.
You can find some work in branch sequence_gcc_theorical_dist.
I didn't find a good way to display about dialog. Even in CuteVCF.
About dialog should contains application Logo and Labsquare Logo .
Then several Tab widget to show License, Authors , Credits .
A link button to github will be greate.
Not having to pull in Java is already a great advantage of FastQT over FastQC, but dealing with dependencies manually can be a hassle.
A binary release or a package would be A+.
Thanks!
Maybe just add fonction for save and load the future report format.
Create Sequence Length Distribution Analysis According : FastQC Module
I didn't read the code from fastqc.
How to compute a tristate value for each analysis ( Good - medium - Bad) .
This status will display the icons close to th analysis
make an easy way to access Analysis from class Name .
runner->analysis(className) .
Create Per Base N Content according FastQC Module
add recent files in File Menu
see http://doc.qt.io/qt-4.8/qt-mainwindows-recentfiles-example.html
Reach analysis has a status which indicate the quality. See #31
It would be nice to have the sum of those status to display on the list view. I don't know how to compute it.
Maybe use only one of them.
On the Tableview, as @ikit said, align colname to the left
No 0.2 when this bug isn't close.
The code of this analysis is bugged, use fastq file with just 75 bp length read to see the bug.
This analysis required a complete or partial rewrite, I find some stupid end useless code.
Hi,
I work with 3th generation of sequencing, in this generation all read didn't have the same length.
So for Per Base Content graph (its an example) the end of graph become chaotic because the information is support just by a little bit of sequence.
May be we can add coverage information by color gradiant on background of the graph.
Thank for your work.
Users don't necessarily have a .fastq<.gz/etc> extension on their FASTQ files - .fq / .fq.gz / .trim / etc are also common - users should be able to choose what to load in. This might be OK as a default, but at least there should be an option to display 'All files' in the file browser when loading files for analysis. This also impacts the drag-and-drop functionality.
Add font awesome to style application
Hi,
@junebs report to a problem durring the install phase of make.
Version : devel branch
Distributon : Manjaro
Error message :
sudo make install
install -m 755 -p fastqt /usr/local/bin/fastqt
strip /usr/local/bin/fastqt
install -m 755 -p /media/DATA/Projects/fastQt/fastqt.desktop /usr/share/applications/
strip /usr/share/applications/fastqt.desktop
strip:/usr/share/applications/fastqt.desktop: Format de fichier non reconnu
make: [Makefile:1141: install_desktop] Error 1 (ignorée)
install -m 755 -p /media/DATA/Projects/fastQt/fastqt.png /usr/share/icons/hicolor/48x48/apps/
strip /usr/share/icons/hicolor/48x48/apps/fastqt.png
strip:/usr/share/icons/hicolor/48x48/apps/fastqt.png: Format de fichier non reconnu
make: [Makefile:1151: install_icons] Error 1 (ignorée)
I didn't repoduce this bug on Fedora 25
we should be able to run FastQt from console .
That's mean exporting graph into png.
Put StatusBar in mainWindow and display the elapsed time
@ysard help me to create a snap file from master branch !
http://snapcraft.io/create/
In some comment we can see reference to QUazip but we replace this by KArchive.
I little clean up and check if commented code do important think is require.
Some analysis hasn't yet status indicator.
Do it like : https://github.com/labsquare/fastQt/blob/devel/analysis/perbasequalityanalysis.cpp#L205
Try :
touch file.fastq
And try to open it.
It's important. Several pipeline produce empty file. We should avoid a crash just for this.
As @ikit suggest : some documentation is required.
For instance, some context menu etc..
Set a Thread parmaters for the analysis Runner model, to allow if fixed number of file which can be process simultanously.
Open multiple files ! One per thread
Enable drop file from desktop to fastqt
Create per Sequence GC content according FASTQC Module
Using Qt linguistic it would be easy.
Just issue to list little thing need to be check before run the release 0.2.
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