Preliminary commit of a more inclusive get_nearest_Gene method using Nathan’s largely unedited code.
Up to minimum working state. Code runs, test data ready, but no useful tests yet.
Maximum search distance identified as necessary, and exclusion of self from the results.
Rename of method to respect adaptor naming conventions, cleanup, and minor steps toward test data.
Exception for inappropriate values of $prime
when going downstream, comparison is based on feature end
when going upstream, comparison is based on feature start
Tabs… what an unpleasant surprise
Restore edge case test, rename variable.
s/tab/in the eye/
Bonus debug tests.
Mr Tab has proven to be quite an adversary.
Working rewrite of fetch_all_nearest_by_Feature using the API rather than SQL statements. Partially tested but needs some finessing and comments.
Documentation updates and explanatory notes.
Slippery sigils.
All cases working, some tested, lots of documentation. Still needs the sign to be inverted on distances.
Corrections for reverse-stranded comparisons, more tests. Still doesn't work for distance calculations on neighbouring assembly segments.
Final change made to correctly compute cross-seq-region distances, a few more tests.
homo_sapiens/patch/transcript.txt: SQLite does not like header.
exon.t: ignore 'datatype mismatch' bind errors on floating point for SQLite.
dbEntries.t: correct offset in SQLite auto-increment munging.