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cleaned up GPU consensus calling #1

Merged
merged 115 commits into from
Oct 3, 2019
Merged

cleaned up GPU consensus calling #1

merged 115 commits into from
Oct 3, 2019

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hasindu2008
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This pull request restructures and cleans up the changes so that:

  1. it can be automatically merged to nanopolish; and,
  2. changes to original nanopolish code and behaviour are minimised.

hasindu2008 and others added 30 commits December 16, 2017 13:49
@hasindu2008
removed unnecessary parts in scrappie to get compiled on arm
1e1e77a
@hasindu2008
Merge branch 'fast5_rewrite'
d4bad59
@hasindu2008
Merge remote-tracking branch 'upstream/master'
f8e473d
@hasindu2008
comment to makefile
418bbc1
Update not to run ".depend" task when running "make clean".
21e4909
@jts
do not rely on split() to parse window string since the contig name m…
8f2a4d9 
…ay contain "=" characters
@jts
Merge branch 'master' of https://github.com/jts/nanopolish
af3ac82
@jts
Merge branch 'feature/makefile-clean-depends-tasks' of https://github…
212ed72 
….com/junaruga/nanopolish into junaruga-feature/makefile-clean-depends-tasks
@jts
Merge branch 'junaruga-feature/makefile-clean-depends-tasks'
3ab666d
@jts
emit missing genotype when there are no reads
5a4939d
Refactor Makefile to build with specified version's dependencies.
e484cf7
sync with jts
c5b9341
fix builtin header
f6e1c08
@jts
vcf2fasta: add option -f to read from a fofn
01e1438
@hasindu2008
one dimensional array patch for faster multithreaded performance
0ef7c25
@jts
remove std::vector implementation
267315f
@jts
remove some whitespace
3137ba2
@jts
Merge branch 'hasindu2008-cppvector_to_1darray'
004daa4
@jts
Merge pull request jts#466 from junaruga/feature/set-dependency-version
f7600ad 
Update to build with specified version's dependencies.
@jts
update makefile to fix jts#465
50e8b5c
@jts
Merge branch 'master' of https://github.com/jts/nanopolish
d7c09ab 
Conflicts:
	Makefile
@paultsw
add a quickstart tutorial for the polya subprogram
c124bcb
@jts
Merge pull request jts#517 from paultsw/master
85f4f01 
add a quickstart tutorial for the polya subprogram
@jts
refactor fast5 io to use a struct with a bit of state
14de733
@mike-molnar
Update training to use multiset logsum
526f894
@mike-molnar
Update training to use multiset logsum
29cbd52
@jts
support variable-length string attributes
346f000
@jts
nanopolish index now supports multi-fast5
011f129
@jts
finish support for multi-fast5 files
1ba48bd
@jts
Merge pull request jts#476 from isaclee/master
027aa97 
Adding GpC call functionality
jts and others added 29 commits June 13, 2019 09:21
@jts
do not load reads that do not have their sequence in the bam
17010c6
@jts
remove stl_algo include (closes jts#612)
67d072d
@jts
fix call-methylation help string (jts#604)
08e6432
@jts
clean up vcf2fasta --skip-checks to handle the case where there are n…
6b644f6 
…o windows for a contig (jts#611)
@jts
Merge branch 'master' of https://github.com/jts/nanopolish
1f5dfd8
@jts
update to htslib-1.9
b171671
@jts
attempt to fix build by not requiring lzma for htslib
06c9d38
@jts
downgrade htslib until I can figure out dependency issues
b431872
@jts
downgrade HDF to 1.8 to avoid flock() issues reported by users
db8b04f
@johnomics
Fix filehandle and name references
e31834a 
Commit ee6b01d broke this script as it introduced new variable names but didn't change the old usages. This commit fixes the names.
@jts
Merge pull request jts#624 from johnomics/johnomics-patch-1
1d6828e 
Fix filehandle and name references
@jts
fix off-by-one in contig coordinates (jts#623)
42112b2
@jts
Merge branch 'master' of https://github.com/jts/nanopolish
6331dc4
@jts
fix calculate_methylation_frequency usage
8d1ba76
@Shians
Update manual.rst
17b16b1 
Slight rewording of the output content.
@jts
Merge pull request jts#639 from Shians/patch-1
1e31418 
Update manual.rst
@paultsw
add helper scripts to facilitate the poly(A)-HMM retraining process
42487a1
@paultsw
run 2to3 to make compatible with python3
b4b4748
@paultsw
change python invocations to python3
d557a44
@hasindu2008
changes to the makefile to get it compiled
f3bf3e1
@hasindu2008
cleaned up the make file and added cuda support as an option with min…
e484b29 
…imal changes to the original source
@hasindu2008
Merge remote-tracking branch 'upstream/master' into gpu-varcall
c0fe717
@hasindu2008
cleaned up to be consistent with the original code
f19f9b8
@hasindu2008
restructured to minimise changes to the original source code
5658597
@hasindu2008
make the --gpu more clear
8338b92
@hasindu2008
Merge remote-tracking branch 'upstream/master' into gpu-varcall-update
3c8677b
@hasindu2008
set to cuda static runtime library
c05733b
@hasindu2008
removed .gitignore in test/
8964db0
@hasindu2008
add cida object file to make file clean option
896b806
@iiSeymour iiSeymour merged commit 0fa62cd into nanoporetech:candidate-scoring-gpu Oct 3, 2019
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9 participants
@hasindu2008 @iiSeymour @jts @paultsw @mike-molnar @kpalin @wdecoster @johnomics @Shians