MashMap v3.0.6 #58

bkille · 2023-07-10T17:57:59Z

--splitPrefix now performs the filtering on each prefix-group independently.
Does not sketch or winnow k-mers w/ ambiguous nucleotides.
Added kc:f tag for the estimated k-mer complexity, defined as the ratio of the estimated number of distinct k-mers in a segment to the total number of k-mers in a segment (this estimate can be greater than 1.0).
Added a flag --kmerComplexity x to filter out segments with estimated kmer complexity less than x.
Mapping progress now updates for each segment mapped, as opposed to each contig mapped.
Added --reportPercentage option to report ANI as a percentage instead of in [0, 1] range (necessary for use w/ wfmash)
Fixes Compilation issues under Archlinux using cmake #54
Does not split sequences smaller than the block length.
Added address sanitizer for Debug build

bkille added 15 commits June 29, 2023 15:13

Add option to report ANI as percentage in [0, 100]

671fc42

add missing include

d586a03

Add address sanitizer for debug

38f3e38

Working split-prefix filter

b9bf235

Fix missing include found in #54

efce4ec

Update version number

3045335

Ignore k-mers w/ ambiguous nucleotides

f7c4856

Do not split sequences smaller than the block length

f17cf64

Only filter once and after chaining

7bc4d40

Add predicted sequence complexity tag (sc:f:x.xx)

e9b82f6

make length mismatch filter optional

cc85484

Remove string view

0ac569a

Remove debug code

1db87ea

Add kmer complexity filter

0ce0c7d

Make progcontainer a child class

b440e04

bkille merged commit 4f4df5d into master Jul 10, 2023

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