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reporting on number of sequences with 'sourmash compute --merge' is wrong #352

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ctb opened this issue Oct 2, 2017 · 1 comment · Fixed by #351
Closed

reporting on number of sequences with 'sourmash compute --merge' is wrong #352

ctb opened this issue Oct 2, 2017 · 1 comment · Fixed by #351

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@ctb
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ctb commented Oct 2, 2017

sourmash compute -k 31 shew-reads/contigs.fa.gz shew-reads.nocontigs.fa --scaled 1000 -o shew-reads.nocontigs.fa.both.sig --merge=combined 
setting num_hashes to 0 because --scaled is set
computing signatures for files: shew-reads/contigs.fa.gz, shew-reads.nocontigs.fa
Computing signature for ksizes: [31]
Computing only DNA (and not protein) signatures.
Computing a total of 1 signatures.
... reading sequences from shew-reads/contigs.fa.gz
... shew-reads/contigs.fa.gz 320000... reading sequences from shew-reads.nocontigs.fa
calculated 1 signatures for 6601 sequences taken from shew-reads/contigs.fa.gz shew-reads.nocontigs.fa

also note that we need a line break when switching files.

@ctb
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ctb commented Mar 11, 2018

More reproducible:

sourmash compute -k 31 data/*.fna.gz -o zzz --merge foo

reports

calculated 1 signatures for 78 sequences taken from data/GCF_000005845.2_ASM584v2_genomic.fna.gz data/GCF_000006945.1_ASM694v1_genomic.fna.gz data/GCF_000783305.1_ASM78330v1_genomic.fna.gz

but

gunzip -c data/*.fna.gz | grep ^'>' | wc -l

reports 81 sequences.

ctb added a commit that referenced this issue Mar 11, 2018
luizirber pushed a commit that referenced this issue Mar 12, 2018
* clear to eol in notify(...) and error(...)
* clean up --merge compute output
* more printout cleanup
* add test to verify fix for #352
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