ErrMerr stuff, small changes

Author: BrettKennedy

.gitignore

@@ -39,3 +39,4 @@ utilBMF/cFqProc.c
 utilBMF/cstring.c
 Doc/*
 BMFTools.egg-info/*
+Bin/*

SecC/ArrayHeatmap2D.py

@@ -30,13 +30,13 @@
 r2data = np.array(r2data)
 
 fig, ax = plt.subplots(figsize=(15,10))
-plt.suptitle("Observed Quality by Cycle and Nucleotide (Read 2)")
-heatmap = ax.pcolormesh(np.transpose(r2data), cmap=plt.cm.Blues)
+plt.suptitle("Observed Quality by Cycle and Nucleotide (Read 1)")
+heatmap = ax.pcolormesh(np.transpose(r1data), cmap=plt.cm.Blues)
 cbar = fig.colorbar(heatmap, label="Observed Quality")
 ax.axis('tight')
 ax.set_yticks([0.5, 1.5, 2.5, 3.5])
 ax.set_yticklabels(["A","C","G","T"])
 plt.xlabel("Cycle (Position in Read)")
 plt.ylabel("Nucleotide")
-plt.savefig("ErrorArrayHeatmapRead2.png")
+plt.savefig("ErrorArrayHeatmapRead1.png")
 plt.show()

SecC/ArrayHeatmap3D.py

@@ -36,11 +36,11 @@
 r2data = np.array(r2data)
 
 fig, ax = plt.subplots(figsize=(15,10))
-plt.suptitle("Observed Quality by Illumina Quality and Cycle (Read 1)")
-heatmap = ax.pcolormesh(np.transpose(r1data), cmap=plt.cm.Reds)
+plt.suptitle("Observed Quality by Illumina Quality and Cycle (Read 2)")
+heatmap = ax.pcolormesh(np.transpose(r2data), cmap=plt.cm.Reds)
 cbar = fig.colorbar(heatmap, label="Observed Quality")
 ax.axis('tight')
 plt.xlabel("Cycle (Position in Read)")
 plt.ylabel("Illumina Given Quality Score")
-plt.savefig("CycleQualityHeatmapRead1.png")
+plt.savefig("CycleQualityHeatmapRead2.png")
 plt.show()

SecC/ErrMerr.py

@@ -150,6 +150,7 @@ def cycleError(args):
         flag = read.flag
         if flag & 2820:
             continue
+            qc += 1
         """
         Equivalent to:
         if(read.is_secondary or read.is_supplementary or