Fixed merge conflicts.

.gitignore

@@ -4,6 +4,7 @@
 *.so
 .tox
 .DS_Store
+.idea
 _trial_temp
 __pycache__
 build

CHANGELOG.md

@@ -3,6 +3,16 @@
 Dropped the `FastaFaiIndex` class. Use `SqliteIndex` instead. Fixed two
 skipped Python 3 tests (for gzipped and bz2'd file reading).
 
+## 3.1.88 February 02, 2021
+
+Another attempt to fix the bug in bowtie2 that was introduced by adding the
+`--removePrimersFromBedFile` option to `run-bowtie2.py`.
+
+## 3.1.87 February 02, 2021
+
+Fixed bug in bowtie2 that was introduced by adding the
+`--removePrimersFromBedFile` option to `run-bowtie2.py`.
+
 ## 3.1.86 January 31, 2021
 
 Fixed two failing tests due to changed DIAMOND (version 2.0.6) bitscore

dark/__init__.py

@@ -7,4 +7,4 @@
 # will not be found by the version() function in ../setup.py
 #
 # Remember to update ../CHANGELOG.md describing what's new in each version.
-__version__ = '3.1.87'
+__version__ = '3.1.88'

dark/bowtie2.py

@@ -166,10 +166,12 @@ def removePrimers(self, bedFile):
             raise ValueError('makeBAM() has not yet been called.')
 
         self._report("removing primers specified in %s" % bedFile)
+        tempTrimmedBamPrefix = "%s.trimmed" % self._bamFile
         self._executor.execute(
-            "ivar trim -b %s -p result-trimmed -i %s -q 20 -m 30 -s 4 -e" %
-            (bedFile, self._bamFile))
-        self._executor.execute("mv result-trimmed.bam '%s'" % self._bamFile)
+            "ivar trim -b '%s' -p '%s' -i '%s' -q 20 -m 30 -s 4 -e" %
+            (bedFile, tempTrimmedBamPrefix, self._bamFile))
+        self._executor.execute("mv '%s'.bam '%s'" %
+                               (tempTrimmedBamPrefix, self._bamFile))
 
     def markDuplicatesPicard(self, picardFile):
         """