labsquare / cutevcf Goto Github PK

Currently, CuteVcf support native icons theme for Linux according freedesktop specification
But This is not working for windows.

I suggest to create the same icons theme for all OS. That's mean we should provide Icons in the deployment.
Awesome font ? FatCow icons ? @ikit @it-s what do you suggest ?

Shoud be able to open recent from file > open ..

A widget to show raw headers data .
window > show header ?

hello,thanks for the good work with cute variant :). i'm looking for a software to look for annovar output file.
annovar is a classical variant annotation software, it can be great to support tsv annovar output format.

for each region selected, plot a graph according http://vcf.iobio.io/

Create a widget which contains all chromosom avaible.
Double click on chromosom will set the region

In the view, format position ( align left ) and split by 3 digit
12234234 => 12'234'234

get info field types from header and display it with icons / color

CuteVcf should be able to query multi region . For exemple :
chr2:1-10000, chr3:3-2000

And thats mean the possibility to filter using bed file.

otherwise it's freezing the UI with heavy VCF file

You should be able to filter based on column name.

We should be able to export the current variants and all variant.
file>export > all variant
file>export > current view

open and close methods should be avaible !

You should be able to see which column you want to see

Should be able to open non bgzip file .
I suggest to compress it before reading .

I m not sure about the license .. I m using htslib as a dynamics library .
@Arkanosis Which opensource license can I use ?

add : copy genome coordinaite

Support ANN fields name .
See :
http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf

Would be nice to have generic link editor to open variant.
For exemple https://varsome.com

Hi, first beta test! Installation and launch on linux (Fedora 25)

Add the fact to use git clone --recursive in the Readme, I've not fully read your mail, and I missed this information to install correctly ^^

For the compilation, after using qmake, I obtained "./CuteVCF: error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory" when I tried to launch the program with just ./CuteVCF.
However, it work very well via QtCreator.

Finally, when launch, I've not the little chromosome illustration and colors show in your preview.

About dialog is not finished..
need : Licenses, authors , github button

See thread for context https://www.biostars.org/p/227973/#232095

After adding
QMAKE_CXXFLAGS += -std=c++11

I get the following error when running make:

~/Downloads/CuteVCF$ make
g++ -Wl,-O1 -Wl,-rpath,/home/wdecoster/anaconda3/lib -o CuteVCF qfonticon.o aboutdialog.o createindexdialog.o infowidget.o mainwindow.o main.o qtabix.o samplewidget.o vcfheader.o vcfline.o vcfmodel.o qrc_files.o moc_qfonticon.o moc_aboutdialog.o moc_createindexdialog.o moc_infowidget.o moc_mainwindow.o moc_samplewidget.o moc_vcfmodel.o   -L/home/wdecoster/Downloads/CuteVCF/htslib -lhts -L/home/wdecoster/anaconda3/lib -lQt5Widgets -lQt5Gui -lQt5Concurrent -lQt5Core -lGL -lpthread 
qtabix.o: In function `QTabix::buildIndex(QString const&)':
qtabix.cpp:(.text+0x313): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
qtabix.o: In function `QTabix::open()':
qtabix.cpp:(.text+0x703): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
qtabix.cpp:(.text+0x763): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
qtabix.cpp:(.text+0x7a3): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
qtabix.o: In function `QTabix::readInfo()':
qtabix.cpp:(.text+0x10d3): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
qtabix.o:qtabix.cpp:(.text+0x1113): more undefined references to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)' follow
collect2: error: ld returned 1 exit status
Makefile:219: recipe for target 'CuteVCF' failed
make: *** [CuteVCF] Error 1

$ qmake --version
QMake version 3.0
Using Qt version 5.6.0 in /home/wdecoster/anaconda3/lib

About dialog should display markdown syntax

Parse all variant and count how many A>T, C>G etc...
Plot a Pie

• Remove dockwidget border : http://stackoverflow.com/questions/40594721/qt-padding-margins-in-dockable-windows

• Put Search bar above the table view only.

@it-s Could you check the gif animation on the main page and make me some suggestion ?
Thanks

With UCSC, Ensembl , IGV ...
A contextual menu when you click on variant .

Hello,
The method you just give to install qt in the read me is not working for me. The ppa seem to be broken. you may suggest to install through the website.
Aurelien

Display info dialog !
file format , filedate, source, reference etc....
All ##key=value