Add option to filter according to strand.

scripts/bed_bam2fq.py

@@ -13,7 +13,7 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
-"""Extracts the fastq reads from a bam file
+"""Extract the fastq reads from a bam file
 corresponding to the annotations provided in a bed file.
 """
 
@@ -38,6 +38,12 @@ def main():
         "-a", "--bamfile",
         required=True,
         help="Input bam file.")
+    parser.add_argument(
+        "-s", "--strand",
+        default="Any",
+        choices=["Any", "Same", "Opposite"],
+        help="Choose hether to keep all reads or only "
+        "those on one strand with respect to bed annotations.")
     args = parser.parse_args()
 
     bamfile = BamFile(args.bamfile)