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synchronization with vgteam's fork#3

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ekg wants to merge 58 commits intoocxtal:masterocxtal/dozeu:masterfrom vgteam:mastervgteam/dozeu:masterCopy head branch name to clipboard

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Commits

Commits on Apr 13, 2020

• start making gap length configurable

  jeizenga

  committed
  4a28493

Commits on Apr 14, 2020

• make max gap len configurable for each read

  jeizenga

  committed
  bccbe0b

Commits on Apr 15, 2020

• Merge pull request #1 from vgteam/new-features

  Show description for f6d71ca
  jeizenga

  authored
  f6d71ca

Commits on Apr 17, 2020

• start writing qual adj preprocessor flags

  jeizenga

  committed
  848d998

Commits on Apr 22, 2020

• first draft of qual adj flag

  jeizenga

  committed
  7d5a519

• only include unittests without qual adj

  jeizenga

  committed
  d598123

Commits on Apr 24, 2020

• debug quality adjusted xdrop alignment

  jeizenga

  committed
  b5e9f91

• Merge pull request #2 from vgteam/qual-adj-flag

  Show description for 1f8ec0a
  jeizenga

  authored
  1f8ec0a

Commits on Apr 27, 2020

• preserve memory alignment when packing qual values

  jeizenga

  committed
  f38c0ff

• Merge pull request #3 from vgteam/fix-qual-packing

  Show description for e752fe1
  jeizenga

  authored
  e752fe1

Commits on Apr 28, 2020

• fix bugs in DP and traceback

  jeizenga

  committed
  afd7708

• Merge pull request #4 from vgteam/bug-fixes

  Show description for 7dbc148
  jeizenga

  authored
  7dbc148

• fix traceback bug

  jeizenga

  committed
  dac13b1

Commits on Jun 25, 2020

• Remove unnecessary ifdef around __SSE4_1__

  Show description for 180db30
  

  nemequ

  authored and

  mr-c

  committed
  180db30

• Use <smmintrin.h> instead of <x86intrin.h>

  Show description for f21411d
  

  nemequ

  authored and

  mr-c

  committed
  f21411d

• Allow alternate implementations of the SSE4.1 API.

  

  nemequ

  authored and

  mr-c

  committed
  73c1d2b

Commits on Jun 26, 2020

• use the SIMD Everywhere library

  mr-c

  committed
  0ba4f19

Commits on Jul 1, 2020

• fix small bug in dp

  jeizenga

  committed
  d87c266

• Merge pull request #6 from vgteam/dp-bug

  Show description for e084ecd
  jeizenga

  authored
  e084ecd

Commits on Jul 7, 2020

• Merge pull request #5 from mr-c/simde

  Show description for 5bfca0e
  adamnovak

  authored
  5bfca0e

Commits on Jul 10, 2020

• incorporate full length bonus into dp

  jeizenga

  committed
  9d1e905

• Merge pull request #7 from vgteam/full-length-dp

  Show description for 39e45db
  jeizenga

  authored
  39e45db

Commits on Jul 14, 2020

• Use a simde that builds on Clang 11

  adamnovak

  committed
  10d70a7

• Merge pull request #8 from vgteam/clang11

  Show description for 2ded4c1
  adamnovak

  authored
  2ded4c1

• Avoid complaints about extern C templates from simde

  adamnovak

  committed
  d0e6efe

• Merge pull request #9 from vgteam/clang11

  Show description for 56fdff0
  adamnovak

  authored
  56fdff0

Commits on Jul 28, 2020

• handle xdrops between two non-xdrop vectors

  jeizenga

  committed
  89c8e1e

• Merge pull request #10 from vgteam/xdrop-bug

  Show description for eabdf60
  jeizenga

  authored
  eabdf60

Commits on Oct 12, 2020

• allow full length bonus to be selected per read

  jeizenga

  committed
  d8c2d86

• Merge pull request #11 from vgteam/flb-per-read

  Show description for 6b6a5cd
  jeizenga

  authored
  6b6a5cd

Commits on Jan 22, 2021

• fix traceback over x-dropped vectors

  jeizenga

  committed
  01ba10e

• Merge pull request #12 from vgteam/xdrop-traceback

  Show description for 8baec71
  jeizenga

  authored
  8baec71

Commits on Jan 23, 2021

• maintain two separate ranges for forward and backward in forefront

  jeizenga

  committed
  54578f1

• Merge pull request #13 from vgteam/xdrop-traceback

  Show description for b4ad142
  jeizenga

  authored
  b4ad142

Commits on Feb 28, 2022

• use fast indexing for constant qual values

  jeizenga

  committed
  17e3896

Commits on Mar 1, 2022

• Merge pull request #14 from vgteam/qual-indexing

  Show description for 632954e
  jeizenga

  authored
  632954e

Commits on Sep 7, 2023

• Start trying to run Dozeu tests; notice that root which they use has been removed

  adamnovak

  committed
  b40572b

Commits on Sep 8, 2023

• Get Dozeu examples to use the new dz_alignment_init_s

  adamnovak

  committed
  9e9c39f

• Add allocator documentation and avoid possible free space overflow

  adamnovak

  committed
  ead027d

• Start allocating a bit with runs

  adamnovak

  committed
  0115be5

• Change dst semantics

  adamnovak

  committed
  f2eab2c

• Explain more about caps

  adamnovak

  committed
  9e65cb4

• Explain about the above-the-stack range logic we use

  adamnovak

  committed
  614e35a

• Clarify the loop relationship

  adamnovak

  committed
  18f98e7

• Explain matrix structure more

  adamnovak

  committed
  2fe9393

• Refactor around a stream with reservations and break traceback

  adamnovak

  committed
  46e9820

• Add debugging and remember to actually allocate the head cap

  adamnovak

  committed
  370dab3

• Stop early unwinding

  adamnovak

  committed
  9282fc7

Commits on Sep 18, 2023

• Add more logging and rip out unsafe debugging stack arrays

  adamnovak

  committed
  1e0d445

Commits on Oct 10, 2023

• Account for columns possibly needing to end in forefronts, and stop if reservations are wrong

  adamnovak

  committed
  05412de

• Remove extra debugging

  adamnovak

  committed
  d15473f

• Remove wayward parenthese

  adamnovak

  committed
  fc57037

• Account for the dz_head_s when guessing column sizes

  adamnovak

  committed
  1a70aec

Commits on Nov 22, 2023

• Make dz_flush actually consistent with dz_init

  adamnovak

  committed
  8d27629

• Make example demo using flush

  adamnovak

  committed
  b8edacf

• Add a way to limit retained memory in a dz_s without remaking it

  adamnovak

  committed
  3625c99

• Stop logging stack

  adamnovak

  committed
  c7dce48

Commits on May 30, 2024

• Merge pull request #15 from vgteam/alloc-better

  Show description for 999a0ed
  adamnovak

  authored
  999a0ed