Fix up "consume_X_and_WHATEVER" functions

dib-lab / khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

http://khmer.readthedocs.io/

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Fix up "consume_X_and_WHATEVER" functions #1029

Open kdm9 opened 9 years ago

kdm9 commented 9 years ago

This is largely for my own reference, stuff I've discovered during #1016 and #1017:

Hashtable::consume_fasta_and_tag doesn't use imprint_next_read, or catch NoMoreReadsAvailable
Ditto to consume_fasta_and_tag_with_stoptags
And consume_partitioned_fasta

Should I try and at least catch NoMoreReadsAvailable in these functions as part of #1017, @mr-c or @ctb? (also, is @Blahah working on this code [lib/hashtable.{cc,hh}])

Cheers, K

(P.S., I'll add to the above list)

blahah commented 9 years ago

I have no plans to do anything on hashtable.{cc,hh}.

ctb commented 9 years ago

@kdmurray91 anything you do would be much appreciated!

kdm9 commented 9 years ago

Also fasta_dump_kmers_by_abundance and fasta_count_kmers_by_position have similar issues. There's quite a tight correlation between places which don't catch NoMoreReadsAvailable and those that still use get_next_read.

kdm9 commented 9 years ago

Ditto to output_fasta_kmer_pos_freq

kdm9 commented 9 years ago

Will split this into two PRs: ensuring NoMoreReadsAvailable is caught I'll do as part of #1017. I'll make another PR consigning get_next_read to history, as I have time, but hopefully before 2.0 :smile:

kdm9 commented 9 years ago

Also consume_fasta_and_traverse

mr-c commented 9 years ago

Sounds great!

mr-c commented 9 years ago

Ping @kdmurray91 :-)

kdm9 commented 9 years ago

Ahh, forgot about this. Is anyone (read @ctb) going to mind if this is a post-2.0 issue?

mr-c commented 9 years ago

Already tagged post-2.0 :-)