Avoid passing too many parameters.

[haowenz]

NOTE: this PR would change MAPQ for single-end and Hi-C mappings.

This code refactor helped identify and fix bugs for single-end read and Hi-C read MAPQ. It is clear that the parameters were passed in the wrong order, which led to wrong MAPQ for single-end reads at the following line.

chromap/src/mapping_generator.h

Line 858 in 3ce2414

kNegative, num_negative_candidates, repetitive_seed_length, mapq,

For Hi-C reads, the bug is at the following line.

chromap/src/mapping_generator.h

Line 1089 in 3ce2414

negative_mappings1, negative_split_sites1, num_positive_candidates2,

Here num_positive_candidates2 should be num_negative_candidates2.

After fixing this, the single-end simulated read MAPQ seems to get improved as shown in the following figure.

Tested on all benchmark datasets. No change on paired-end ChIP-seq or scATAC-seq mappings was observed. Hi-C mappings only slightly changed. And the MAPQ of many single-end ChIP-seq mappings changed.

Reducing the parameters for verification functions seems to cause the change of single-end mappings and a few good single-end mappings were missed. But when running Chromap on a single missed read, the mapping of it was reported. Thus, this might be a problem cause by cache. So this PR will be examined again after @mourisl fix the cache.

[haowenz]

Checked again after the cache was fixed. The single-end mappings look okay. So merge this PR.