[MRG] Fix multigather so that the output CSV contains all matches.
#2322
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@@ Coverage Diff @@
## latest #2322 +/- ##
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+ Coverage 84.84% 92.14% +7.30%
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Files 131 100 -31
Lines 15689 11420 -4269
Branches 2190 2191 +1
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- Hits 13311 10523 -2788
+ Misses 2083 602 -1481
Partials 295 295
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ctb
changed the title
multigather so that the output CSV contains all matches.multigather so that the output CSV contains all matches.
ctb
changed the title
multigather so that the output CSV contains all matches.multigather so that the output CSV contains all matches.
…o fix/multigather_indent
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@sourmash-bio/devs @dkoslicki ready for review! |
dkoslicki
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Oct 14, 2022
This was referenced Aug 19, 2023
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Aug 21, 2023
Note: PR into #2065. This PR updates #2065 with all the changes from `latest`. This includes the fix & update to multigather in #2322, which: - fixes the output of multigather to include more than one line 😆 - prints out the output filename - supports `--output-dir` No functional changes are made beyond the merge, so some tests are still failing; will discuss fixes in yet a new PR :). --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Keya Barve <53328492+keyabarve@users.noreply.github.com> Co-authored-by: ccbaumler <63077899+ccbaumler@users.noreply.github.com> Co-authored-by: Tessa Pierce Ward <bluegenes@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Taylor Reiter <taylorreiter@gmail.com> Co-authored-by: Erik Young <eeyoung@ucdavis.edu> Co-authored-by: David Koslicki <dmkoslicki@gmail.com> Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com> Co-authored-by: Colton Baumler <baumlerc@farm.ucdavis.edu> Co-authored-by: Luiz Irber <contact+github@luizirber.org> Co-authored-by: N. Tessa Pierce-Ward <ntpierce@gmail.com> Co-authored-by: Peter Cock <p.j.a.cock@googlemail.com> Co-authored-by: Francesco Beghini <francesco.beghini@yale.edu> Co-authored-by: Jason Stajich <jason.stajich@ucr.edu> Co-authored-by: Katrin Leinweber <9948149+katrinleinweber@users.noreply.github.com>
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This PR fixes #2321 so that more than one output line is placed in the CSV. Oops!
It also adds a notification of what the CSV output file name is.
Last but not least, it supports
--output-diras a way to set the base path for all output files.Fixes #2321.
TODO:
multigatherCSV output uses signaturefilenameas basename. #2328