Merge branch 'master' of gitlab.pasteur.fr:bli/libhts

requirements.txt

+Cython
+libworkflows @ git+https://gitlab+deploy-token-31:isEzpsgbNf2sJMdUDy2g@gitlab.pasteur.fr/bli/libworkflows.git
+matplotlib
+networkx
+numpy
+pandas
+pyBigWig
+pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option="cythonize"
+scipy
+seaborn

scripts/sam2indexedbam.sh

@@ -31,6 +31,7 @@ function error_exit
 samtools --version
 
 SAM=${1}
+echo "Will sort and index ${SAM}"
 
 case ${SAM} in
     *.sam)

setup.py

@@ -28,7 +28,7 @@ setup(
         "numpy",
         "pandas",
         "pyBigWig",
-        "pybedtools",
+        "pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers",
         "scipy",
         "seaborn"],
     # specific versions and index would rather belong to requirements.txt