Several changes by joshuak94 · Pull Request #37 · seqan/vaquita

joshuak94 · 2019-10-14T10:57:36Z

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

Submodules

…ument_parser of seqan2.

Arg parser

Add seqan:: to everything.

Add option for long reads

Add a few fixes for the command options.

… to include sviper.

… TODO: Figure out how to merge breakpoint managers and retain information.

…ads should be used.

… combined.

…nd pairedend breakpoints if it is short read manager, or if the short read input file was not given.

Sviper on long read

…plit and maxOverlap for long reads.

…nput.

…and long reads.

…lts are reported based on how confident the variant call is.

… private member access.

joshuak94 and others added 30 commits October 24, 2018 17:31

Added seqan3 submodule

79d988b

update seqan3 submodule

5304649

[INTERNAL] Adds seqan3 into the cmake files.

443819b

switch hardcoded seqan with submodule

47a7825

Merge pull request #1 from joshuak94/submodules

edea3e1

Submodules

Phase in the argument_parser of seqan3 and replace completely the arg…

c06edc0

…ument_parser of seqan2.

Terminate main program if any step returns false.

713c6a1

fix seqan3::argument_parser bugs

baeedec

Merge pull request #2 from joshuak94/arg_parser

23b42ff

Arg parser

Add option for long reads

6c3764e

Add seqan:: to everything.

45a5b83

Merge pull request #3 from joshuak94/remove_namespace

2de9b0a

Add seqan:: to everything.

Merge pull request #4 from joshuak94/long_read_input_only

bd3c733

Add option for long reads

Make the output file an option.

8af9a10

Merge pull request #5 from joshuak94/option_fixes

b4b0cea

Add a few fixes for the command options.

Add SViper as a submodule. Update other submodules, update CMakeLists…

8562348

… to include sviper.

Put calling of SViper commands into vaquita.cpp.

85f4543

Introduce implicit conversion from VcfRecordEnhanced to Variant.

30aefa6

Prevent overwriting of info, quality and filter if they aren't empty.

46d2c48

Change the printing message to use seqan3:;debug_steram

de6bc16

Allow alignment to choose between long and short reads

a84da94

Beginning of long read integration

43ef35e

Separate alignment and breakpoint managers into long and short reads.…

849ac40

… TODO: Figure out how to merge breakpoint managers and retain information.

Enable merging of long read breakpoints into short read breakpoints.

290bc0a

Create alignmentManager with boolean to indiciate if long or short re…

6e01142

…ads should be used.

Change RUN_IF macro to set bool to true if condition not satisfied.

f9ce7b5

add null pointer check to pbamfileout

db70bdc

Small fix to output of evidences found and fix to how breakpoints are…

efa033e

… combined.

Change from deleting lr breakpoints to just iterating to next one.

03a95c0

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 and others added 6 commits November 14, 2019 10:12

Fix how ref_chrom is set for the Variant object.

5ef8dd8

Add SE definition to output header.

dc8dddc

Run SViper only if short and long reads are given.

8d9cde2

Set skipped variants to pass.

4754143

Add openmp to packages for compiling.

e04f4cb

Merge pull request #8 from joshuak94/sviper_on_long_read

47b5edd

Sviper on long read

joshuak94 mentioned this pull request Nov 14, 2019

seqan3 argument parser #36

Closed

Output sum of SE, CE, and PE when merging. Also create a default maxS…

2e47376

…plit and maxOverlap for long reads.

joshuak94 force-pushed the develop branch from db25637 to 2e47376 Compare November 22, 2019 13:21

joshuak94 and others added 9 commits November 25, 2019 16:06

Create default maxSplit and maxOverlap values specific to long read i…

9489bb6

…nput.

small fix

ce9113e

Temporarily use origin/develop for sviper

b55c158

Introduce option to set thread count.

246d377

More seqan namespace fixes.

64febc8

Print out maxSplitLong and maxOverlapLong, and make SViper toggleable

682a881

Use UpdateBreakpoint instead of AddNewBreakpoint for combining short …

626fb11

…and long reads.

Only filter out SViper FAIL5 id.

3335db2

Add more info to pass on to SViper, and switch how strict SViper resu…

3b5d834

…lts are reported based on how confident the variant call is.

joshuak94 force-pushed the develop branch from c74365a to 3b5d834 Compare November 29, 2019 09:02

joshuak94 added 2 commits November 29, 2019 12:42

Undo temporary checkout of SViper.

d7652ea

Create another check on updating variant based on long read coverage.

b30c062

joshuak94 force-pushed the develop branch from b67a6d9 to b30c062 Compare November 29, 2019 15:50

joshuak94 and others added 4 commits November 29, 2019 16:52

fix

06c0173

Move long read coverage to own function.

5e81258

Calculate short read length in Vaquita and pass on to SViper.

343fc21

Update sviper and print sviper header to log.

4471d67

joshuak94 force-pushed the develop branch from 1c3bf60 to 4471d67 Compare December 1, 2019 17:05

joshuak94 and others added 3 commits December 3, 2019 13:42

update sviper

9ce02b0

update sviper

1a03584

Update Seqan and Seqan3 submodules, update minimum CMake version, fix…

6813311

… private member access.

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Several changes#37

Several changes#37
joshuak94 wants to merge 60 commits into
seqan:develop_longreadfrom
joshuak94:develop

joshuak94 commented Oct 14, 2019

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joshuak94 commented Oct 14, 2019

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