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Set default shrink block offset #23

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Set default shrink block offset #23

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4 changes: 3 additions & 1 deletion scripts/kraken-build
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,7 @@ $ENV{"PATH"} = "$KRAKEN_DIR:$ENV{PATH}";
my $DEF_MINIMIZER_LEN = 15;
my $DEF_KMER_LEN = 31;
my $DEF_THREAD_CT = 1;
my $DEF_SHRINK_BLOCK_OFFSET = 1;

my @VALID_LIBRARY_TYPES = qw/bacteria plasmids viruses human/;

Expand Down Expand Up @@ -68,6 +69,7 @@ my (
$threads = $DEF_THREAD_CT;
$minimizer_len = $DEF_MINIMIZER_LEN;
$kmer_len = $DEF_KMER_LEN;
$shrink_block_offset = $DEF_SHRINK_BLOCK_OFFSET;
$work_on_disk = "";
$hash_size = "";
$max_db_size = "";
Expand Down Expand Up @@ -232,7 +234,7 @@ Options:
(build task only)
--shrink-block-offset NUM When shrinking, select the k-mer that is NUM
positions from the end of a block of k-mers
(default: 1)
(def: $DEF_SHRINK_BLOCK_OFFSET)
--work-on-disk Perform most operations on disk rather than in
RAM (will slow down build in most cases)
EOF
Expand Down