[MRG] adjust output of gather to indicate weighted/unweighted results

[ctb]

This PR adjusts the output of gather so that it's clear whether the coverage is abundance-weighted or not.

The full output is below, but the only changed line is:

for unweighted / --ignore-abundance:
the recovered matches hit 34.8% of the query (unweighted)

for weighted:
the recovered matches hit 35.3% of the abundance-weighted query

Full output below.

Some decisions I made in this PR:

• it would be ideal to print out both unweighted and weighted numbers, but I don't think we track them internally. see provide both abundance-weighted coverage & flattened coverage in sourmash gather output? #1818 for issue.
• I decided to change both unweighted and weighted output strings so that it would be easy to tell if we were looking at output from a version of sourmash that included this change.

Fixes #1805.

cc #1818

full output

with -p abund sketch -

== This is sourmash version 4.2.4.dev0+g73aeb155.d20220116. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

select query k=31 automatically.
loaded query: gut.cluster.41.fa.gz.cdbg_ids.... (k=31, DNA)
loaded 1 databases.

Starting prefetch sweep across databases.
Found 4 signatures via prefetch; now doing gather.

overlap     p_query p_match avg_abund
---------   ------- ------- ---------
134.0 kbp      7.6%    4.3%       1.9    FR883346.1 Clostridium sp. CAG:221 ge...
114.0 kbp     27.7%    3.0%       9.0    MARQ01000035.1 Clostridium perfringen...
found less than 50.0 kbp in common. => exiting

found 2 matches total;
the recovered matches hit 35.3% of the abundance-weighted query

with --ignore-abundance:

== This is sourmash version 4.2.4.dev0+g73aeb155.d20220116. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

select query k=31 automatically.
loaded query: gut.cluster.41.fa.gz.cdbg_ids.... (k=31, DNA)
loaded 1 databases.

Starting prefetch sweep across databases.
Found 4 signatures via prefetch; now doing gather.

overlap     p_query p_match
---------   ------- -------
134.0 kbp     19.5%    4.3%    FR883346.1 Clostridium sp. CAG:221 ge...
114.0 kbp     15.3%    3.0%    MARQ01000035.1 Clostridium perfringen...
found less than 50.0 kbp in common. => exiting

found 2 matches total;
the recovered matches hit 34.8% of the query (unweighted)

[ctb]

@drtamermansour @bluegenes @mr-eyes thoughts on this change? it's small but very useful.

[codecov]

Codecov Report

Merging #1819 (ec7e297) into latest (4f9d17d) will increase coverage by 6.67%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           latest    #1819      +/-   ##
==========================================
+ Coverage   83.48%   90.15%   +6.67%     
==========================================
  Files         113       87      -26     
  Lines       12181     8482    -3699     
  Branches     1626     1627       +1     
==========================================
- Hits        10169     7647    -2522     
+ Misses       1754      577    -1177     
  Partials      258      258              

Flag	Coverage Δ
python	90.15% <100.00%> (+<0.01%)	⬆️
rust	?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/sourmash/commands.py	88.24% <100.00%> (+0.02%)	⬆️
src/core/src/ffi/signature.rs
src/core/src/encodings.rs
src/core/src/ffi/mod.rs
src/core/src/sketch/hyperloglog/estimators.rs
src/core/src/ffi/hyperloglog.rs
src/core/src/cmd.rs
src/core/src/errors.rs
src/core/src/index/search.rs
src/core/src/ffi/cmd/compute.rs
... and 17 more

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[bluegenes]

I think this will be very helpful!

[drtamermansour]

This is VERY useful.
I suggested using the string "abundance ignored" instead of "unweighted" to be more informative.