Strandedness fix depends on bedtools version.

Also updated dependencies

libbamutils/__init__.py

 __copyright__ = "Copyright (C) 2020 Blaise Li"
 __licence__ = "GNU GPLv3"
-__version__ = 0.7
+__version__ = 0.8
 from .libbamutils import (
     BamFile, BedFile,
     filter_read_size,

libbamutils/libbamutils.py

@@ -21,7 +21,7 @@ from itertools import dropwhile, takewhile
 from operator import attrgetter
 from cytoolz import merge_with
 # To get coordinates of genes
-from libhts import id_list_gtf2bed
+from libhts import BEDTOOLS_VERSION, id_list_gtf2bed
 # To collapse aligned reads to their 5' ends
 from bam25prime import (
     collapse_and_sort,
@@ -60,6 +60,20 @@ def filter_read_size(alis, min_len=None, max_len=None):
         yield ali
 
 
+# To correctly preserve strand information after merging records
+# See https://bioinformatics.stackexchange.com/q/15834/292
+[major, minor, patch] = BEDTOOLS_VERSION[1:].split("."))
+if (major, minor) >= (2, 27):
+    # s=True: Force strandedness.
+    # That is, only merge features that are on the same strand
+    # Otherwise, strand information is lost
+    # With 2.27 and above, it seeùs this is not enough.
+    # Column 7 in gtf contains strand information.
+    merge_kwds = {"s": True, c: 7, o: "distinct"}
+else:
+    merge_kwds = {"s": True}
+
+
 def get_gene_intervals(gene_list_filename, annot_filename, id_kwd=None):
     """
     Obtain the bed coordinates of the genomic regions covered by
@@ -79,10 +93,8 @@ def get_gene_intervals(gene_list_filename, annot_filename, id_kwd=None):
     return id_list_gtf2bed(
         gene_identifiers, annot_filename,
         id_kwd=id_kwd).sort().merge(
-            # s=True: Force strandedness.
-            # That is, only merge features that are on the same strand
-            # Otherwise, strand information is lost
-            s=True, stream=True)
+            **merge_kwds,
+            stream=True)
 
 
 # TODO: allow different upstream and downstream maximum distances

setup.py

@@ -20,6 +20,8 @@ setup(
     packages=find_packages(),
     install_requires=[
         "bam25prime @ git+https://gitlab.pasteur.fr/bli/bam25prime.git",
+        "cytoolz",
+        "libhts @ git+https://gitlab.pasteur.fr/bli/libhts.git",
         "libreads @ git+https://gitlab.pasteur.fr/bli/libreads.git"])
     #ext_modules = cythonize("libsmallrna/libsmallrna.pyx"),
     #install_requires=["cytoolz"],