ksw2

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Potential feature request : Fitting / infix alignment

2

Hi @lh3, It would be very useful to us to have support in ksw2 for "infix" or "fitting" alignment, where they query aligns within the target, but the precise starting...

rob-p

Comment on https://github.com/lh3/ksw2/blob/4e0a1ccba8c6ccc87e0342c9712531bde783bf90/ksw2_extd2_sse.c#L255 (and similar comments below) should read `d |= a > 0? 1

mimaric

Possibly not calculating s array in ksw_extd2_see() correctly

2

In `ksw_extd2_see()` if valid elements of an antidiagonal have target indices in range `[st0, en0]` all elements in `[st=st0/16*16, en=(en0+16)/16*16-1]` are going to be processed, i.e. all elements within 16-element...

mimaric

I am comparing the behavior of `ksw_extd()` and `ksw_extd2_sse()`. One difference I noticed is the case when `tlen > qlen + w`, i.e. when target is long enough for some...

mimaric

Dear Heng (@lh3), First of all, I would like to thank you for developing such an awesome library for aligning biological sequences. We (+ @rob-p and @fataltes) are using ksw2...

mohsenzakeri

Hi I have been using ksw_exts2_sse with following parameters: int noncan = 9; q = 4; e = 2; q2 = 32; zdrop = 200; flag = 1600; and I...

jmaricb

Hi, I'm trying copilling ksw2 to use [Salmon](https://salmon.readthedocs.io/en/latest/building.html) in ARM ubuntu (aarch), but I'm getting the following error: ``` rock01 ksw2 # make gcc -c -g -Wall -Wextra -Wc++-compat -O2...

patrick-douglas

Hi, When I test gg2_sse using the following command: ./ksw2-test -t gg2_sse test/q2.fa.gz test/t2.fa.gz. but it reports an error: Segmentation fault (core dumped) So, could you give me some suggestions...

moold

Thanks for publishing this library! How burdensome would it be to support = and X characters in the output CIGAR strings instead of the canonical M character?

standage