Mqf integration2

[shokrof]

MQF, Mixed Quotient Filter, is a new variant of CQF. MQF has changed the counting scheme of the parent data structure by adding fixed size counters and using a different encoding for the dynamic one.
This improvement makes MQF more memory efficient for a wider range of Zipfian distributions. Also, MQF expanded the metadata component of the filter to enable tagging of its kmers. In addition to the basic functions provided by the original CQF, the new data structure comes with an expanding list of kmer processing functions including functions for merging and resizing the filter, functions for comparing kmer sets, and functions for indexing and meta-analysis of multiple kmer groups. More details about these functions can be found here

• Is any new functionality in tested? (This can be checked with
  make clean diff-cover or the CodeCov report that is automatically
  generated following a successful CI build.)
• Was a spellchecker run on the source code and documentation after
  changes were made?
• Have any changes to the command-line interface been explicitly described?
  Only backwards-compatible additions are allowed without a major version
  increment. Changing file formats also requires a major version number
  increment.
• Have any substantial changes been documented in CHANGELOG.md? See
  keepachangelog for more details.
• Do the changes respect streaming I/O? (Are they tested for streaming I/O?)

[codecov-io]

Codecov Report

Merging #1873 into master will decrease coverage by <.01%.
The diff coverage is 0%.

@@            Coverage Diff            @@
##           master   #1873      +/-   ##
=========================================
- Coverage    0.07%   0.06%   -0.01%     
=========================================
  Files          67      67              
  Lines        6685    7222     +537     
  Branches     2487     434    -2053     
=========================================
  Hits            5       5              
- Misses       6680    7217     +537

Impacted Files	Coverage Δ
src/oxli/storage.cc	0% <0%> (ø)	⬆️
include/oxli/storage.hh	0% <0%> (ø)	⬆️
src/oxli/hllcounter.cc	0% <0%> (ø)	⬆️
src/oxli/traversal.cc	0% <0%> (ø)	⬆️
src/oxli/assembler.cc	0% <0%> (ø)	⬆️
src/khmer/_cpy_utils.cc	0% <0%> (ø)	⬆️
include/oxli/kmer_hash.hh	0% <0%> (ø)	⬆️
src/khmer/_cpy_khmer.cc	0% <0%> (ø)	⬆️
src/oxli/kmer_hash.cc	0% <0%> (ø)	⬆️
include/oxli/read_parsers.hh	0% <0%> (ø)	⬆️
... and 18 more

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[standage]

DUUUUUUUUUDE!!!! Are those passing tests I see???

[shokrof]

Yes :)
I solved the problem by adding "-stdlib=libc++" and "-nostdinc+" while compiling my c++ library(MQF). Also, I added -lstdc++ while linking.

I am now upgrading the mqf to the latest version and the request will be ready for merging.

[shokrof]

@ctb @standage @drtamermansour
MQF is now ready to be integrated into Khmer.
Please review. I am waiting for your comments.

Have a nice day.
Mostafa

[drtamermansour]

@shokrof I added a description to the pull request but you still need to review the pull request checklist. Also, I think we should reference and close the related pull requests #1859 #1865

[ctb]

hi folks, this looks ready to review - am I right?

[drtamermansour]

Yes. It should be ready to go a while ago.