Unset use of LaTeX, fix read type examination.

libhts/libhts.py

@@ -20,18 +20,19 @@ from scipy.stats.stats import pearsonr, linregress
 from scipy.stats.mstats import gmean
 import matplotlib as mpl
 import matplotlib.pyplot as plt
+# TODO: set this at the "correct" place
 # https://stackoverflow.com/a/42768093/1878788
-from matplotlib.backends.backend_pgf import FigureCanvasPgf
-mpl.backend_bases.register_backend('pdf', FigureCanvasPgf)
-TEX_PARAMS = {
-    "text.usetex": True,            # use LaTeX to write all text
-    "pgf.rcfonts": False,           # Ignore Matplotlibrc
-    "pgf.texsystem": "lualatex",  # hoping to avoid memory issues
-    "pgf.preamble": [
-        r'\usepackage{color}'     # xcolor for colours
-    ]
-}
-mpl.rcParams.update(TEX_PARAMS)
+#from matplotlib.backends.backend_pgf import FigureCanvasPgf
+#mpl.backend_bases.register_backend('pdf', FigureCanvasPgf)
+#TEX_PARAMS = {
+#    "text.usetex": True,            # use LaTeX to write all text
+#    "pgf.rcfonts": False,           # Ignore Matplotlibrc
+#    "pgf.texsystem": "lualatex",  # hoping to avoid memory issues
+#    "pgf.preamble": [
+#        r'\usepackage{color}'     # xcolor for colours
+#    ]
+#}
+#mpl.rcParams.update(TEX_PARAMS)
 import seaborn as sns
 # from rpy2.robjects import r, pandas2ri, Formula, StrVector
 # as_df = r("as.data.frame")
@@ -275,11 +276,22 @@ def aligner2min_mapq(aligner, wildcards):
     What minimal MAPQ value should a read have to be considered uniquely mapped?
     See <https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/>.
     """
+    mapping_type = None
     try:
         mapping_type = wildcards.mapping_type
     except AttributeError:
-        mapping_type = wildcards.mapped_type
-    if mapping_type.startswith("unique_"):
+        pass
+    if mapping_type is None:
+        try:
+            mapping_type = wildcards.mapped_type
+        except AttributeError:
+            pass
+    if mapping_type is None:
+        try:
+            mapping_type = wildcards.read_type
+        except AttributeError:
+            pass
+    if mapping_type is None or mapping_type.startswith("unique_"):
         if aligner == "hisat2":
             return "-Q 60"
         elif aligner == "bowtie2":