Commit 711099aa authored by Blaise Li's avatar Blaise Li
Browse files

Add option to filter according to strand.

parent 5caa8ef3
...@@ -13,7 +13,7 @@ ...@@ -13,7 +13,7 @@
# #
# You should have received a copy of the GNU General Public License # You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>. # 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. corresponding to the annotations provided in a bed file.
""" """
...@@ -38,6 +38,12 @@ def main(): ...@@ -38,6 +38,12 @@ def main():
"-a", "--bamfile", "-a", "--bamfile",
required=True, required=True,
help="Input bam file.") 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() args = parser.parse_args()
bamfile = BamFile(args.bamfile) bamfile = BamFile(args.bamfile)
......
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