.gitignore

+# # Mac
+.DS_STORE
+.env
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

CHANGELOG.md

 # Change log
 All notable changes to this project will be documented in this file.
 
+## Version 2.3.4 2019-01-14
+- TRANSIT:	
+  - Minor bug fixes related to flags in Resampling and HMM
+
 ## Version 2.3.3 2018-12-06
 - TRANSIT:	
   - Minor bug fixes related to flags in HMM

README.md

-# TRANSIT 2.3.3
+# TRANSIT 2.3.4
 
 
 [![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) 

debian/changelog

+tnseq-transit (2.3.4-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper 12
+  * Standards-Version: 4.3.0
+
+ -- Andreas Tille <tille@debian.org>  Wed, 30 Jan 2019 15:54:42 +0100
+
 tnseq-transit (2.3.3-1) unstable; urgency=medium
 
   * New upstream version

debian/compat

-11
+12

debian/control

@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
                dh-python,
                python-dev,
                python-setuptools,
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),
                python-matplotlib,
                python-statsmodels,
                bwa
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/tnseq-transit
 Vcs-Git: https://salsa.debian.org/med-team/tnseq-transit.git
 Homepage: http://saclab.tamu.edu/essentiality/transit/

src/pytransit/__init__.py

@@ -2,6 +2,6 @@
 __all__ = ["transit_tools", "tnseq_tools", "norm_tools", "stat_tools"]
 
 
-__version__ = "v2.3.3"
+__version__ = "v2.3.4"
 prefix = "[TRANSIT]"
 

src/pytransit/analysis/hmm.py

@@ -226,6 +226,7 @@ class HMMMethod(base.SingleConditionMethod):
         normalization = wxobj.hmmNormChoice.GetString(wxobj.hmmNormChoice.GetCurrentSelection())
 
         LOESS = False
+        LOESS = wxobj.hmmLoessCheck.GetValue()
 
         #Get output path
         name = transit_tools.basename(ctrldata[0])
@@ -377,6 +378,8 @@ class HMMMethod(base.SingleConditionMethod):
         self.output.write("# \n")
         self.output.write("# Mean:\t%2.2f\n" % (numpy.average(reads_nz)))
         self.output.write("# Median:\t%2.2f\n" % numpy.median(reads_nz))
+        self.output.write("# Normalization:\t%s\n" % self.normalization)
+        self.output.write("# LOESS Correction:\t%s\n" % str(self.LOESS))
         self.output.write("# pins (obs):\t%f\n" % pins_obs)
         self.output.write("# pins (est):\t%f\n" % pins)
         self.output.write("# Run length (r):\t%d\n" % r)

src/pytransit/analysis/resampling.py

@@ -219,6 +219,7 @@ class ResamplingMethod(base.DualConditionMethod):
 
         base.DualConditionMethod.__init__(self, short_name, long_name, short_desc, long_desc, ctrldata, expdata, annotation_path, output_file, normalization=normalization, replicates=replicates, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
 
+        self.Z = False
         self.samples = samples
         self.adaptive = adaptive
         self.doHistogram = doHistogram
@@ -316,7 +317,6 @@ class ResamplingMethod(base.DualConditionMethod):
         includeZeros = not excludeZeros
         pseudocount = float(kwargs.get("pc", 0.00))
 
-        self.Z = False
         if "Z" in kwargs: self.Z = True    
         
         LOESS = kwargs.get("l", False)