Avoid repetitive syncmers

[marcelm]

This is only to document how results would change when avoiding repetitive syncmers. These two commits were originally part of #464, but I removed them because the effect is so small.

Changes are relative to #464.

Comparing accuracy (paf)

92c6105 Produce a syncmer if any minimum is at the required position
48b8257 Sample fewer syncmers in repetitive regions

library	92c6105	48b8257	difference
sim5-drosophila-50-se	76.9434	76.9428	-0.0006
sim5-drosophila-75-se	83.4574	83.4662	+0.0088
sim5-drosophila-100-se	84.9698	85.0006	+0.0308
sim5-drosophila-150-se	87.5199	87.5247	+0.0048
sim5-drosophila-200-se	89.2588	89.2764	+0.0176
sim5-drosophila-300-se	91.2808	91.2698	-0.0110
sim5-maize-50-se	39.1029	39.0660	-0.0369
sim5-maize-75-se	51.1972	51.1828	-0.0144
sim5-maize-100-se	58.7602	58.7517	-0.0085
sim5-maize-150-se	70.7971	70.7977	+0.0006
sim5-maize-200-se	77.6729	77.6700	-0.0029
sim5-maize-300-se	84.6080	84.6204	+0.0124
sim5-CHM13-50-se	74.2958	74.3139	+0.0181
sim5-CHM13-75-se	82.7271	82.7352	+0.0081
sim5-CHM13-100-se	85.3325	85.3486	+0.0161
sim5-CHM13-150-se	88.6368	88.6345	-0.0023
sim5-CHM13-200-se	90.4160	90.4165	+0.0005
sim5-CHM13-300-se	92.1565	92.1592	+0.0027
sim5-rye-50-se	36.5431	36.5321	-0.0110
sim5-rye-75-se	49.1549	49.1423	-0.0126
sim5-rye-100-se	57.3552	57.3367	-0.0185
sim5-rye-150-se	69.9844	70.0066	+0.0222
sim5-rye-200-se	76.9929	77.0022	+0.0093
sim5-rye-300-se	83.8594	83.8577	-0.0017
sim5-ecoli50-50-se	10.7365	10.7364	-0.0001
sim5-ecoli50-75-se	13.6556	13.6550	-0.0006
sim5-ecoli50-100-se	15.8174	15.8174	+0.0000
sim5-ecoli50-150-se	20.0893	20.0893	+0.0000
sim5-ecoli50-200-se	23.3933	23.3933	+0.0000
sim5-ecoli50-300-se	28.3073	28.3060	-0.0013

Average difference se: +0.0010

Comparing accuracy (paf)

92c6105 Produce a syncmer if any minimum is at the required position
bb384f8 Ignore repetitive k-mers

library	92c6105	bb384f8	difference
sim5-drosophila-50-se	76.9434	76.9176	-0.0258
sim5-drosophila-75-se	83.4574	83.4443	-0.0131
sim5-drosophila-100-se	84.9698	84.9998	+0.0300
sim5-drosophila-150-se	87.5199	87.5099	-0.0100
sim5-drosophila-200-se	89.2588	89.2666	+0.0078
sim5-drosophila-300-se	91.2808	91.2886	+0.0078
sim5-maize-50-se	39.1029	39.0993	-0.0036
sim5-maize-75-se	51.1972	51.1967	-0.0005
sim5-maize-100-se	58.7602	58.7662	+0.0060
sim5-maize-150-se	70.7971	70.8051	+0.0080
sim5-maize-200-se	77.6729	77.6560	-0.0169
sim5-maize-300-se	84.6080	84.5989	-0.0091
sim5-CHM13-50-se	74.2958	74.2933	-0.0025
sim5-CHM13-75-se	82.7271	82.7352	+0.0081
sim5-CHM13-100-se	85.3325	85.3485	+0.0160
sim5-CHM13-150-se	88.6368	88.6354	-0.0014
sim5-CHM13-200-se	90.4160	90.4067	-0.0093
sim5-CHM13-300-se	92.1565	92.1479	-0.0086
sim5-rye-50-se	36.5431	36.5736	+0.0305
sim5-rye-75-se	49.1549	49.1517	-0.0032
sim5-rye-100-se	57.3552	57.3378	-0.0174
sim5-rye-150-se	69.9844	69.9829	-0.0015
sim5-rye-200-se	76.9929	76.9919	-0.0010
sim5-rye-300-se	83.8594	83.8475	-0.0119
sim5-ecoli50-50-se	10.7365	10.7351	-0.0014
sim5-ecoli50-75-se	13.6556	13.6575	+0.0019
sim5-ecoli50-100-se	15.8174	15.8174	+0.0000
sim5-ecoli50-150-se	20.0893	20.0910	+0.0017
sim5-ecoli50-200-se	23.3933	23.3906	-0.0027
sim5-ecoli50-300-se	28.3073	28.3059	-0.0014

Average difference se: -0.0008

[marcelm]

This was only for documentation, closing.