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synchronization with vgteam's fork #3

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synchronization with vgteam's fork #3

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4a28493
start making gap length configurable
jeizenga Apr 13, 2020
bccbe0b
make max gap len configurable for each read
jeizenga Apr 14, 2020
f6d71ca
Merge pull request #1 from vgteam/new-features
jeizenga Apr 15, 2020
848d998
start writing qual adj preprocessor flags
jeizenga Apr 17, 2020
7d5a519
first draft of qual adj flag
jeizenga Apr 22, 2020
d598123
only include unittests without qual adj
jeizenga Apr 22, 2020
b5e9f91
debug quality adjusted xdrop alignment
jeizenga Apr 24, 2020
1f8ec0a
Merge pull request #2 from vgteam/qual-adj-flag
jeizenga Apr 24, 2020
f38c0ff
preserve memory alignment when packing qual values
jeizenga Apr 27, 2020
e752fe1
Merge pull request #3 from vgteam/fix-qual-packing
jeizenga Apr 27, 2020
afd7708
fix bugs in DP and traceback
jeizenga Apr 28, 2020
7dbc148
Merge pull request #4 from vgteam/bug-fixes
jeizenga Apr 28, 2020
dac13b1
fix traceback bug
jeizenga Apr 28, 2020
180db30
Remove unnecessary ifdef around __SSE4_1__
nemequ Feb 9, 2020
f21411d
Use <smmintrin.h> instead of <x86intrin.h>
nemequ Feb 9, 2020
73c1d2b
Allow alternate implementations of the SSE4.1 API.
nemequ Feb 9, 2020
0ba4f19
use the SIMD Everywhere library
mr-c Jun 25, 2020
d87c266
fix small bug in dp
jeizenga Jul 1, 2020
e084ecd
Merge pull request #6 from vgteam/dp-bug
jeizenga Jul 1, 2020
5bfca0e
Merge pull request #5 from mr-c/simde
adamnovak Jul 7, 2020
9d1e905
incorporate full length bonus into dp
jeizenga Jul 10, 2020
39e45db
Merge pull request #7 from vgteam/full-length-dp
jeizenga Jul 10, 2020
10d70a7
Use a simde that builds on Clang 11
adamnovak Jul 14, 2020
2ded4c1
Merge pull request #8 from vgteam/clang11
adamnovak Jul 14, 2020
d0e6efe
Avoid complaints about extern C templates from simde
adamnovak Jul 14, 2020
56fdff0
Merge pull request #9 from vgteam/clang11
adamnovak Jul 14, 2020
89c8e1e
handle xdrops between two non-xdrop vectors
jeizenga Jul 28, 2020
eabdf60
Merge pull request #10 from vgteam/xdrop-bug
jeizenga Jul 28, 2020
d8c2d86
allow full length bonus to be selected per read
jeizenga Oct 12, 2020
6b6a5cd
Merge pull request #11 from vgteam/flb-per-read
jeizenga Oct 12, 2020
01ba10e
fix traceback over x-dropped vectors
jeizenga Jan 22, 2021
8baec71
Merge pull request #12 from vgteam/xdrop-traceback
jeizenga Jan 22, 2021
54578f1
maintain two separate ranges for forward and backward in forefront
jeizenga Jan 23, 2021
b4ad142
Merge pull request #13 from vgteam/xdrop-traceback
jeizenga Jan 23, 2021
17e3896
use fast indexing for constant qual values
jeizenga Feb 28, 2022
632954e
Merge pull request #14 from vgteam/qual-indexing
jeizenga Mar 1, 2022
b40572b
Start trying to run Dozeu tests; notice that root which they use has …
adamnovak Sep 7, 2023
9e9c39f
Get Dozeu examples to use the new dz_alignment_init_s
adamnovak Sep 8, 2023
ead027d
Add allocator documentation and avoid possible free space overflow
adamnovak Sep 8, 2023
0115be5
Start allocating a bit with runs
adamnovak Sep 8, 2023
f2eab2c
Change dst semantics
adamnovak Sep 8, 2023
9e65cb4
Explain more about caps
adamnovak Sep 8, 2023
614e35a
Explain about the above-the-stack range logic we use
adamnovak Sep 8, 2023
18f98e7
Clarify the loop relationship
adamnovak Sep 8, 2023
2fe9393
Explain matrix structure more
adamnovak Sep 8, 2023
46e9820
Refactor around a stream with reservations and break traceback
adamnovak Sep 8, 2023
370dab3
Add debugging and remember to actually allocate the head cap
adamnovak Sep 8, 2023
9282fc7
Stop early unwinding
adamnovak Sep 8, 2023
1e0d445
Add more logging and rip out unsafe debugging stack arrays
adamnovak Sep 18, 2023
05412de
Account for columns possibly needing to end in forefronts, and stop i…
adamnovak Oct 10, 2023
d15473f
Remove extra debugging
adamnovak Oct 10, 2023
fc57037
Remove wayward parenthese
adamnovak Oct 10, 2023
1a70aec
Account for the dz_head_s when guessing column sizes
adamnovak Oct 10, 2023
8d27629
Make dz_flush actually consistent with dz_init
adamnovak Nov 22, 2023
b8edacf
Make example demo using flush
adamnovak Nov 22, 2023
3625c99
Add a way to limit retained memory in a dz_s without remaking it
adamnovak Nov 22, 2023
c7dce48
Stop logging stack
adamnovak Nov 22, 2023
999a0ed
Merge pull request #15 from vgteam/alloc-better
adamnovak May 30, 2024
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4 changes: 4 additions & 0 deletions .gitmodules
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
[submodule "simde"]
path = simde
url = https://github.com/nemequ/simde-no-tests
branch = 2931676
2 changes: 1 addition & 1 deletion Makefile
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@

CC=gcc
OFLAGS=-O3
CFLAGS=$(OFLAGS) -std=c99 -Wall -Wno-unused-variable -Wno-unused-function -march=native
CFLAGS=$(OFLAGS) -std=c99 -Wall -Wno-unused-variable -Wno-unused-function -march=native -g

all: example example.2bit example.protein

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