pmd: sorted order of cpgs in input file

[andrewdavidsmith]

The only criteria we need is for chromosomes to be kept together. It would be much more robust and lead to fewer locale problems if we check that the chrom differs rather than increases to ensure these are kept together.

[guilhermesena1]

This might be worth changing on smithlab_cpp. Right now many of the tools rely on the < operator for GenomicRegion, which uses the lexicographic sorting of chromosome names. We manually solved this on methcounts, bsrate and methstates using unordered maps to keep track of seen chroms, but the code is essentially copy-pasted between programs, so it should be part of, maybe, smithlab_utils or smithlab_os.

[andrewdavidsmith]

Actually, this might not be the best way to go. Looking at the code within pmd.cpp there are different input file formats and these use different functions. But they are not similar enough to the other tools for us to try and factor out those behaviors. Instead the functions for reading data in pmd.cpp need to be cleaned up first, and after that it should be very easy to fix this problem.

[andrewdavidsmith]

Looking briefly at that function, the best way to go is likely to load all the CpG sites from the input file before attempting to bin them at all. This won't be too much of an overhead for space, and we can check to ensure only symmetric CpG sites are used, along with the appropriate order. We can then bin in a separate function, and that would combine the behavior for the array and wgbs data when it comes to binning, so that the only difference is dealing with the specifics of either format.

[andrewdavidsmith]

This issue is fixed as of roughly v1.4 of dnmtools.