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Set a Thread parmaters for the analysis Runner model, to allow if fixed number of file which can be process simultanously.

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.

We need an icon for FastQt. A based template for all labsquare application would be awesome.
@it-s If you do the job, please join idea, mokup here.
@ikit you can do it too .

Following some idea.. If you can mix both picture.

Currently, I have a stupid ugly bird ...

Just issue to list little thing need to be check before run the release 0.2.

• Check all text in app
• merge devel branch in master
• merge master in package branch
• Check Readme.md
  • Change gif (new ui :) )
  • Add command line usage instruction
  • Update compilation instruction
    • For windows
• Communication plan :
  • Write announce tweet :
    • check announce tweet
    • recheck announce tweet
    • rerecheck announce tweet
  • Write thanks message (dev, packager, designer, tester)
• Web page of tool (report in future)

Here is how I made the main view for the next release 0.2.
tell me what do you thinks ?

See :
https://github.com/labsquare/fastQt/wiki/Command%20Line%20Argument

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.

All in the title !

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.

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.

Put StatusBar in mainWindow and display the elapsed time

we should be able to run FastQt from console .
That's mean exporting graph into png.

During counting reads number, There is no information.. And times doesn't run.

Step to reproduce

Open a Huge fastq.bz2 . It keeps 0 percent without showing anything.

Create Per Base N Content according FastQC Module

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/6%20Per%20Base%20N%20Content.html

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.

Drop file doesn't work with extension containing dot.
For exemple : mytest.sample.fastq.gz cannot be dropped

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 ?

Enable drop file from desktop to fastqt

Do FastQC module .
see :
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/9%20Overrepresented%20Sequences.html

Change color or icon layout .. It's ugly actually, almost for windows
See @ikit advice

Use Quazip

add recent files in File Menu
see http://doc.qt.io/qt-4.8/qt-mainwindows-recentfiles-example.html

As @ikit suggest : some documentation is required.
For instance, some context menu etc..

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

On the Tableview, as @ikit said, align colname to the left

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.

Add font awesome to style application

Create per Sequence GC content according FASTQC Module

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/5%20Per%20Sequence%20GC%20Content.html

Exporting graph each graph as png .
Exporting all analyse as pdf

make an easy way to access Analysis from class Name .

runner->analysis(className) .

If you want this functionality is implement please add comment.

You can find some work in branch sequence_gcc_theorical_dist.

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.

Actualy we use the last extension in filename to choose the compression format, we can replace it by read the magic number.

• gz : 1f 8b (2 bytes)
• bz2 : 'BZ' (16 bytes)
• xz : { 0xFD, '7', 'z', 'X', 'Z', 0x00 } (6 bytes)

For check if file is fastq just read the first character of first 4 lines -> @, [a-Z], +, [.]

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

As follow :

Open multiple files ! One per thread

Drop fastq file from FS to the main view keep analysis at 0 %/

Maybe just add fonction for save and load the future report format.

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.

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.

@ysard help me to create a snap file from master branch !
http://snapcraft.io/create/

Using Qt linguistic it would be easy.

Some analysis hasn't yet status indicator.
Do it like : https://github.com/labsquare/fastQt/blob/devel/analysis/perbasequalityanalysis.cpp#L205

I have to close the windows to do anything else.

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

Create Sequence Length Distribution Analysis According : FastQC Module

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!