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minimap2 2.13 accepts empty sequence IDs #252

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tseemann opened this issue Oct 19, 2018 · 0 comments
Closed

minimap2 2.13 accepts empty sequence IDs #252

tseemann opened this issue Oct 19, 2018 · 0 comments

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@tseemann
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Related to #111

tseemann@trillian:mm2 $ cat seq.fa

>
ATGCATGCATGCATGC
ATGCATGCATGCATGC
ATGCATGCATGCATGC
ATGCATGCATGCATGC
ATGCATGCATGCATGC
ATGCATGCATGCATGC
ATGCATGCATGCATGC

tseemann@trillian:mm2 $ minimap2 -d seq.fa.mmi seq.fa

[M::mm_idx_gen::0.002*1.55] collected minimizers
[M::mm_idx_gen::0.002*1.84] sorted minimizers
[M::main::0.003*1.56] loaded/built the index for 1 target sequence(s)
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.003*1.56] distinct minimizers: 1 (0.00% are singletons); average occurrences: 48.000; average spacing: 2.333
[M::main] Version: 2.13-r850
[M::main] CMD: minimap2 -d seq.fa.mmi seq.fa
[M::main] Real time: 0.004 sec; CPU: 0.006 sec; Peak RSS: 0.003 GB

tseemann@trillian:mm2 $ minimap2 seq.fa seq.fa 2> /dev/null | cut -f 1-10

        112     1       112     +               112     1       112     111
        112     2       112     -               112     2       112     110
        112     1       109     -               112     1       109     108
        112     5       112     +               112     1       108     107
        112     1       108     +               112     5       112     107
        112     1       105     -               112     1       105     104
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