Commit a2b7d313 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.1.1

parent c21a7ae6

.gitignore

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# C extensions

*.so



#atom files

*.nfs*

# Distribution / packaging

.Python

env/

.travis.yml

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language: python



matrix:

  include:

    - os: linux

      dist: trusty

      sudo: required

      python: 2.7

      before_install: "sudo apt-get install -y -f python python-dev python-pip pkg-config python-wxgtk2.8 libpng-dev libjpeg8-dev libfreetype6-dev"

      install: "pip install --upgrade pip setuptools numpy scipy pillow matplotlib pytest"



DISPLAY: 0.0

notifications:

  email:

    on_success: change # default: change

    on_failure: change # default: always

before_script: cd /home/travis/build/mad-lab/transit/tests

script: travis_wait 30 pytest

CHANGELOG.md

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All notable changes to this project will be documented in this file.







## Version 2.1.0 - 2017-06-23

- TRANSIT:

    - Added tooltips next to most parameters to explain their functionality.

    - Added Quality Control window, with choice for normalization method.

    - Added more normalization options to the HMM method.

    - Added LOESS correction functionality back to TRANSIT

    - Added ability to scale Track View based on mean-count of the window.

    - Added ability to scale individual tracks in Track View.

    - Added ability to add tracks of features to Track View.

    - New documentation on normalization.



- TPP:

    - TPP can now accept empty primer prefix (in case reads have been trimmed).

    - TPP can now process reads obtained using Mme1 enzyme and protocol.

    - TPP can now pass flags to BWA.







## Version 2.0.2 - 2016-08-19

    

- TRANSIT:

README.md

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# TRANSIT 2.0





**New in Version 2.0+**

 - Support for Tn5 datasets.

 - New analysis methods.

 - New way to export normalized datasets.



# TRANSIT 2.1.0





[![Build Status](https://travis-ci.org/mad-lab/transit.svg?branch=master)](https://travis-ci.org/mad-lab/transit)   [![Documentation Status](https://readthedocs.org/projects/transit/badge/?version=latest)](http://transit.readthedocs.io/en/latest/?badge=latest) 







**Version 2.1.0 changes (June, 20017)**

- Added tooltips next to most parameters to explain their functionality.

- Added Quality Control window, with choice for normalization method.

- Added more normalization options to the HMM method.

- Added LOESS correction functionality back to TRANSIT

- Added ability to scale Track View based on mean-count of the window.

- Added ability to scale individual tracks in Track View.

- Added ability to add tracks of features to Track View.

- Better status messages for TrackView

- TPP can now accept empty primer prefix (in case reads have been trimmed).

- TPP can now process reads obtained using Mme1 enzyme and protocol.

- TPP can now pass flags to BWA.

- Lots of bug fixes.







**Version 2.0.2 changes (August, 2016)**

- Added support for for custom primers in TPP.
@@ -14,6 +32,12 @@ 
- **New [mailing list](https://groups.google.com/forum/#!forum/tnseq-transit/join)**





**New in Version 2.0+**

 - Support for Tn5 datasets.

 - New analysis methods.

 - New way to export normalized datasets.







Welcome! This is the distribution for the TRANSIT and TPP tools developed by the Ioerger Lab.

VERSION

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version: 2.0.1-58-g0a3b-mod
 
version: 2.1.0-18-g4192-mod