Merge pull request #345 from ksahlin/optimize-kslu

Optimize parameters

CHANGES.md

@@ -2,6 +2,9 @@
 
 ## development version
 
+* #345: Improve mapping accuracy for read lengths <=100 by optimizing
+  parameters. Highest increase is for read length 50, which gains 1-2
+  percentage points accuracy.
 * #293: Fix: When mapping single-end reads, many multimappers were previously
   assigned a high mapping quality. They now get assigned mapping quality zero
   as intended.

src/indexparameters.cpp

@@ -35,12 +35,13 @@ struct Profile {
 static auto max{std::numeric_limits<int>::max()};
 
 static std::vector<Profile> profiles = {
-        Profile{ 50,  90, 20, -4, -3,  2},
-        Profile{100, 110, 20, -4, -2,  2},
-        Profile{125, 135, 20, -4, -1,  4},
+        Profile{ 50,  65, 18, -4, -2, -2},
+        Profile{ 75,  90, 20, -4, -2, -2},
+        Profile{100, 110, 20, -4, -1, -1},
+        Profile{125, 135, 20, -4, -1,  3},
         Profile{150, 175, 20, -4,  1,  7},
-        Profile{250, 275, 20, -4,  4, 13},
-        Profile{300, 375, 22, -4,  2, 12},
+        Profile{250, 275, 22, -4,  4, 14},
+        Profile{300, 375, 22, -4,  3, 13},
         Profile{400, max, 23, -6,  2, 12},
     };
 

tests/phix.pe.paf

@@ -1,11 +1,11 @@
-SRR1377138.37	301	8	254	-	NC_001422.1	5386	800	1046	39	246	255
-SRR1377138.37	301	6	254	+	NC_001422.1	5386	707	955	19	248	255
-SRR1377138.38	301	32	257	-	NC_001422.1	5386	4971	5196	40	225	255
-SRR1377138.38	301	2	219	+	NC_001422.1	5386	4839	5056	30	217	255
+SRR1377138.37	301	8	238	-	NC_001422.1	5386	800	1030	38	230	255
+SRR1377138.37	301	6	254	+	NC_001422.1	5386	707	955	21	248	255
+SRR1377138.38	301	32	239	-	NC_001422.1	5386	4971	5178	39	207	255
+SRR1377138.38	301	2	189	+	NC_001422.1	5386	4839	5026	29	187	255
 SRR1377138.39/1	301	1	259	-	NC_001422.1	5386	1791	2049	45	258	255
 SRR1377138.39/2	301	22	257	+	NC_001422.1	5386	1709	1944	45	235	255
-SRR1377138.40	301	4	265	-	NC_001422.1	5386	3020	3281	40	261	255
-SRR1377138.40	301	3	270	+	NC_001422.1	5386	2957	3224	41	267	255
-rescuable.42	301	4	265	-	NC_001422.1	5386	3020	3281	40	261	255
-rescuable.43	301	3	270	+	NC_001422.1	5386	2957	3224	41	267	255
-not.rescuable	301	4	265	-	NC_001422.1	5386	3020	3281	40	261	255
+SRR1377138.40	301	4	251	-	NC_001422.1	5386	3020	3267	36	247	255
+SRR1377138.40	301	3	267	+	NC_001422.1	5386	2957	3221	37	264	255
+rescuable.42	301	4	251	-	NC_001422.1	5386	3020	3267	36	247	255
+rescuable.43	301	3	267	+	NC_001422.1	5386	2957	3221	37	264	255
+not.rescuable	301	4	251	-	NC_001422.1	5386	3020	3267	36	247	255

tests/phix.se.paf

@@ -1,11 +1,11 @@
-SRR1377138.32	301	2	260	+	NC_001422.1	5386	1434	1692	43	258	255
-SRR1377138.33	301	2	267	+	NC_001422.1	5386	3818	4083	41	265	255
+SRR1377138.32	301	2	257	+	NC_001422.1	5386	1434	1689	41	255	255
+SRR1377138.33	301	2	228	+	NC_001422.1	5386	3818	4044	40	226	255
 SRR1377138.34	301	33	241	-	NC_001422.1	5386	844	1052	37	208	255
 SRR1377138.35	301	5	262	-	NC_001422.1	5386	4041	4298	45	257	255
-SRR1377138.36	301	3	267	+	NC_001422.1	5386	4997	5261	48	264	255
-SRR1377138.37	301	8	254	-	NC_001422.1	5386	800	1046	39	246	255
-SRR1377138.38	301	32	257	-	NC_001422.1	5386	4971	5196	40	225	255
+SRR1377138.36	301	3	263	+	NC_001422.1	5386	4997	5257	47	260	255
+SRR1377138.37	301	8	238	-	NC_001422.1	5386	800	1030	38	230	255
+SRR1377138.38	301	32	239	-	NC_001422.1	5386	4971	5178	39	207	255
 SRR1377138.39/1	301	1	259	-	NC_001422.1	5386	1791	2049	45	258	255
-SRR1377138.40	301	4	265	-	NC_001422.1	5386	3020	3281	40	261	255
-rescuable.42	301	4	265	-	NC_001422.1	5386	3020	3281	40	261	255
-not.rescuable	301	4	265	-	NC_001422.1	5386	3020	3281	40	261	255
+SRR1377138.40	301	4	251	-	NC_001422.1	5386	3020	3267	36	247	255
+rescuable.42	301	4	251	-	NC_001422.1	5386	3020	3267	36	247	255
+not.rescuable	301	4	251	-	NC_001422.1	5386	3020	3267	36	247	255