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Several changes #37

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joshuak94
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  1. Add seqan3 as a submodule.
  2. Switch seqan2 to a submodule as well.
  3. Switch the argument parser to seqan3 instead of seqan2.
  4. Introduce the option for long reads.
  5. Remove the using namespace seqan from everywhere.

joshuak94 and others added 30 commits October 24, 2018 17:31
@joshuak94
Added seqan3 submodule
79d988b
@joshuak94
update seqan3 submodule
5304649
@joshuak94
[INTERNAL] Adds seqan3 into the cmake files.
443819b
@joshuak94
switch hardcoded seqan with submodule
47a7825
@joshuak94
Merge pull request #1 from joshuak94/submodules
edea3e1 
Submodules
@joshuak94
Phase in the argument_parser of seqan3 and replace completely the arg…
c06edc0 
…ument_parser of seqan2.
@joshuak94
Terminate main program if any step returns false.
713c6a1
@joshuak94
fix seqan3::argument_parser bugs
baeedec
@joshuak94
Merge pull request #2 from joshuak94/arg_parser
23b42ff 
Arg parser
@joshuak94
Add option for long reads
6c3764e
@joshuak94
Add seqan:: to everything.
45a5b83
@joshuak94
Merge pull request #3 from joshuak94/remove_namespace
2de9b0a 
Add seqan:: to everything.
@joshuak94
Merge pull request #4 from joshuak94/long_read_input_only
bd3c733 
Add option for long reads
@joshuak94
Make the output file an option.
8af9a10
@joshuak94
Merge pull request #5 from joshuak94/option_fixes
b4b0cea 
Add a few fixes for the command options.
@joshuak94
Add SViper as a submodule. Update other submodules, update CMakeLists…
8562348 
… to include sviper.
@joshuak94
Put calling of SViper commands into vaquita.cpp.
85f4543
@joshuak94
Introduce implicit conversion from VcfRecordEnhanced to Variant.
30aefa6
@joshuak94
Prevent overwriting of info, quality and filter if they aren't empty.
46d2c48
@joshuak94
Change the printing message to use seqan3:;debug_steram
de6bc16
@joshuak94
Allow alignment to choose between long and short reads
a84da94
@joshuak94
Beginning of long read integration
43ef35e
@joshuak94
Separate alignment and breakpoint managers into long and short reads.…
849ac40 
… TODO: Figure out how to merge breakpoint managers and retain information.
@joshuak94
Enable merging of long read breakpoints into short read breakpoints.
290bc0a
@joshuak94
Create alignmentManager with boolean to indiciate if long or short re…
6e01142 
…ads should be used.
@joshuak94
Change RUN_IF macro to set bool to true if condition not satisfied.
f9ce7b5
@joshuak94
add null pointer check to pbamfileout
db70bdc
@joshuak94
Small fix to output of evidences found and fix to how breakpoints are…
efa033e 
… combined.
@joshuak94
Change from deleting lr breakpoints to just iterating to next one.
03a95c0
@joshuak94
Add check for breakpointmanager destructor to only delete splitread a…
86dee99 
…nd pairedend breakpoints if it is short read manager, or if the short read input file was not given.
@joshuak94 joshuak94 mentioned this pull request Nov 14, 2019
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