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base repository: tseemann/abricate
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base: v1.0.0
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head repository: tseemann/abricate
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compare: master
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  • 2 commits
  • 2 files changed
  • 1 contributor

Commits on Apr 19, 2020

  1. Issue #135 | handle > 500 hits

    tseemann committed Apr 19, 2020

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Commits on May 12, 2020

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Showing with 3 additions and 1 deletion.
  1. +1 −0 README.md
  2. +2 −1 bin/abricate
1 change: 1 addition & 0 deletions README.md
Original file line number Diff line number Diff line change
@@ -186,6 +186,7 @@ You can choose a different database using the `--db` option:
## Combining reports across samples

ABRicate can combine results into a simple matrix of gene presence/absence.
An absent gene is denoted `.` and a present gene is represented by its '%COVERAGE`.
This can be individual abricate reports, or a combined one.

```
3 changes: 2 additions & 1 deletion bin/abricate
Original file line number Diff line number Diff line change
@@ -12,7 +12,7 @@ use Cwd qw(abs_path);
#..............................................................................
# Globals needed before --help etc

my $VERSION = "1.0.0";
my $VERSION = "1.0.1";
my $EXE = basename($0);
my $AUTHOR = 'Torsten Seemann';
my $TWITTER = '@torstenseemann';
@@ -124,6 +124,7 @@ for my $file (@ARGV) {
my $cmd = "(any2fasta -q -u \Q$file\E |"
. " $blastcmd -db \Q$db_path\E -outfmt '$format' -num_threads $threads"
. " -evalue 1E-20 -culling_limit $CULL"
. " -max_target_seqs 10000" # https://github.com/tseemann/abricate/issues/135
# . " -max_target_seqs ".$dbinfo->{SEQUENCES} # Issue #76
. ")"
;