Migrate read handling code to utils code.

[standage]

In #1458 and #1435, we added a bunch of generic read handling code to khmer/utils.py, which now has clean_input_reads, broken_paired_iter, and ReadBundle. These should be used to do all Python-based read handling throughout the code.

In particular, all uses of ThreadedSequenceProcessor should be removed; ref #1470.

[ctb]

Here, scripts/filter-abund.py and scripts/filter-abund-single.py would be good targets for a next round of refactoring.

[ctb]

(filter-abund* done in #1469.)

[betatim]

You can now use

from khmer import ReadParser

for index, is_pair, read1, read2 in broken_paired_reader(ReadParser(infile)):
  ...

instead of using screed and benefit from faster reading.