Something I noticed when debugging another issue (which I'll post right after this).

The log reveals what paths names match the pattern: <div class="snippet-clipboard-

--dont_collapse regex behaves weirdly about gfaffix HOT 3 CLOSED

glennhickey commented on September 23, 2024

--dont_collapse regex behaves weirdly

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Comments (3)

danydoerr commented on September 23, 2024

The log reveals what paths names match the pattern:

RUST_LOG=info ../target/release/gfaffix chunk_133493101_133529958_raw.gfa -o chunk_133493101_133529958_fix.gfa --dont_collapse 'CHM13*' > /dev/null
[..]
[2023-11-10T08:06:58Z INFO  gfaffix] flagging nodes of path CHM13#chrX[133493094] as non-collapsing, total number is now at 1017
[..]

and

RUST_LOG=info ../target/release/gfaffix chunk_133493101_133529958_raw.gfa -o chunk_133493101_133529958_fix1.gfa --dont_collapse 'CHM*' > /dev/null
[..]
[2023-11-10T08:07:28Z INFO  gfaffix] flagging nodes of path CHM13#chrX[133493094] as non-collapsing, total number is now at 1017
[2023-11-10T08:07:28Z INFO  gfaffix] flagging nodes of path HG00735#1#JAHBCH010000058.1#0[32659917] as non-collapsing, total number is now at 1431
[..]

So for CHM13*, only path 'CHM13#chrX[133493094]' matches, while for CHM*, also `HG00735#1#JAHBCH010000058.1#0[32659917]' is matched.

This makes perfectly sense, because CHM13* is supposed to match CHM1, CHM13, CHM133, CHM1333, ..., while CHM* matches CH, CHM, CHMM, ...

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glennhickey commented on September 23, 2024

Duh, sorry, should have thought about it for more than a second.

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danydoerr commented on September 23, 2024

NP, glad to help.

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