Pysam issue (#104)

* pip install pysam needs a pip upgrade to complete

* DataFrame deprecated from_items() to from_dict()

* only 2.7 and 3.6 are worth building in the (outdated) trusty environment. Should update to bionic

.travis.yml

@@ -4,7 +4,6 @@ sudo: false
 language: python
 python:
 - '2.7'
-- '3.5'
 - '3.6'
 env: COMPILER_NAME=gcc CXX=g++-5 CC=gcc-5
 addons:
@@ -29,6 +28,7 @@ before_script:
 - pip install future
 - pip install numpy
 - pip install pyomo
+- pip install --upgrade pip
 - pip install pysam
 - pip install matplotlib
 - wget https://support.hdfgroup.org/ftp/HDF5/current18/bin/hdf5-1.8.21-Std-centos7-x86_64-shared_64.tar.gz

hlatyper.py

@@ -236,7 +236,7 @@ def pysam_to_hdf(samfile):
 
     if VERBOSE:
         print('\n', now(), len(hits), 'reads loaded. Creating dataframe...')
-    pos_df = pd.DataFrame.from_items(iter(hits.items())).T
+    pos_df = pd.DataFrame.from_dict(hits, orient='index')
     pos_df.columns = sam.references[:]
     details_df = pd.DataFrame.from_dict(read_details, orient='index')
     details_df.columns = ['mismatches', 'read_length']