added fix mpileup.py scripts to scripts dir in shiva

public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/scripts/fix_mpileup.py

+#!/usr/bin/env python
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+
+from __future__ import print_function
+
+__author__="Wai Yi Leung"
+
+import sys
+
+if __name__ == "__main__":
+    """
+        Fix the mpileupformat for RNA mpileup
+        Solution offered by Irina Pulyakhina (LUMC-HG)
+        http://www.biostars.org/p/78542/
+    """
+    for line in sys.stdin:
+        l = line.strip().split("\t")
+        if l[3] == "0":
+            # no alignment to this position
+            print("\t".join(map(str, l)))
+            continue
+
+        fix_col = l[4].replace('<', '').replace('>', '')
+
+        new_size = len(fix_col)
+        old_size = len(l[4])
+        if new_size != old_size:
+            l[4] = fix_col
+            l[3] = "{}".format(new_size)
+
+        if new_size == 0:
+            l[5] = ""
+
+        print("\t".join(map(str, l)))