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Several changes #37

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Several changes #37

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Commits on Oct 24, 2018

  1. Added seqan3 submodule

    @joshuak94
    joshuak94 committed Oct 24, 2018
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Commits on Jul 24, 2019

  1. update seqan3 submodule

    @joshuak94
    joshuak94 committed Jul 24, 2019
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Commits on Aug 12, 2019

  1. [INTERNAL] Adds seqan3 into the cmake files.

    @joshuak94
    joshuak94 committed Aug 12, 2019
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  2. switch hardcoded seqan with submodule

    @joshuak94
    joshuak94 committed Aug 12, 2019
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  3. Merge pull request #1 from joshuak94/submodules 

    Submodules
    @joshuak94
    joshuak94 authored Aug 12, 2019
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  4. Phase in the argument_parser of seqan3 and replace completely the arg… 

    …ument_parser of seqan2.
    @joshuak94
    joshuak94 committed Aug 12, 2019
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  5. Terminate main program if any step returns false.

    @joshuak94
    joshuak94 committed Aug 12, 2019
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  6. fix seqan3::argument_parser bugs

    @joshuak94
    joshuak94 committed Aug 12, 2019
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  7. Merge pull request #2 from joshuak94/arg_parser 

    Arg parser
    @joshuak94
    joshuak94 authored Aug 12, 2019
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Commits on Oct 8, 2019

  1. Add option for long reads

    @joshuak94
    joshuak94 committed Oct 8, 2019
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Commits on Oct 10, 2019

  1. Add seqan:: to everything.

    @joshuak94
    joshuak94 committed Oct 10, 2019
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  2. Merge pull request #3 from joshuak94/remove_namespace 

    Add seqan:: to everything.
    @joshuak94
    joshuak94 authored Oct 10, 2019
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  3. Merge pull request #4 from joshuak94/long_read_input_only 

    Add option for long reads
    @joshuak94
    joshuak94 authored Oct 10, 2019
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Commits on Oct 16, 2019

  1. Make the output file an option.

    @joshuak94
    joshuak94 committed Oct 16, 2019
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  2. Merge pull request #5 from joshuak94/option_fixes 

    Add a few fixes for the command options.
    @joshuak94
    joshuak94 authored Oct 16, 2019
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  3. Add SViper as a submodule. Update other submodules, update CMakeLists… 

    … to include sviper.
    @joshuak94
    joshuak94 committed Oct 16, 2019
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  4. Put calling of SViper commands into vaquita.cpp.

    @joshuak94
    joshuak94 committed Oct 16, 2019
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  5. Introduce implicit conversion from VcfRecordEnhanced to Variant.

    @joshuak94
    joshuak94 committed Oct 16, 2019
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  6. Prevent overwriting of info, quality and filter if they aren't empty.

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    joshuak94 committed Oct 16, 2019
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Commits on Nov 6, 2019

  1. Change the printing message to use seqan3:;debug_steram

    @joshuak94
    joshuak94 committed Nov 6, 2019
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  2. Allow alignment to choose between long and short reads

    @joshuak94
    joshuak94 committed Nov 6, 2019
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  3. Beginning of long read integration

    @joshuak94
    joshuak94 committed Nov 6, 2019
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  4. Separate alignment and breakpoint managers into long and short reads.… 

    … TODO: Figure out how to merge breakpoint managers and retain information.
    @joshuak94
    joshuak94 committed Nov 6, 2019
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  5. Enable merging of long read breakpoints into short read breakpoints.

    @joshuak94
    joshuak94 committed Nov 6, 2019
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  6. Create alignmentManager with boolean to indiciate if long or short re… 

    …ads should be used.
    @joshuak94
    joshuak94 committed Nov 6, 2019
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  7. Change RUN_IF macro to set bool to true if condition not satisfied.

    @joshuak94
    joshuak94 committed Nov 6, 2019
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  8. add null pointer check to pbamfileout

    @joshuak94
    joshuak94 committed Nov 6, 2019
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  9. Small fix to output of evidences found and fix to how breakpoints are… 

    … combined.
    @joshuak94
    joshuak94 committed Nov 6, 2019
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  10. Change from deleting lr breakpoints to just iterating to next one.

    @joshuak94
    joshuak94 committed Nov 6, 2019
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Commits on Nov 7, 2019

  1. Add check for breakpointmanager destructor to only delete splitread a… 

    …nd pairedend breakpoints if it is short read manager, or if the short read input file was not given.
    @joshuak94
    joshuak94 committed Nov 7, 2019
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  2. Enable writing of breakpoint tsv.

    @joshuak94
    joshuak94 committed Nov 7, 2019
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  3. Add long read contig names if existing.

    @joshuak94
    joshuak94 committed Nov 7, 2019
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Commits on Nov 14, 2019

  1. Merge pull request #6 from joshuak94/sviper_variant_input 

    Add SViper as a functioning submodule.
    @joshuak94
    joshuak94 authored Nov 14, 2019
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  2. Merge pull request #7 from joshuak94/long_read 

    Long read
    @joshuak94
    joshuak94 authored Nov 14, 2019
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  3. Update SViper submodule. Change includes and namespace to reflect upd… 

    …ate.
    @joshuak94
    joshuak94 committed Nov 14, 2019
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  4. Fix how ref_chrom is set for the Variant object.

    @joshuak94
    joshuak94 committed Nov 14, 2019
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  5. Add SE definition to output header.

    @joshuak94
    joshuak94 committed Nov 14, 2019
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  6. Run SViper only if short and long reads are given.

    @joshuak94
    joshuak94 committed Nov 14, 2019
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  7. Set skipped variants to pass.

    @joshuak94
    joshuak94 committed Nov 14, 2019
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  8. Add openmp to packages for compiling.

    @joshuak94
    joshuak94 committed Nov 14, 2019
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  9. Merge pull request #8 from joshuak94/sviper_on_long_read 

    Sviper on long read
    @joshuak94
    joshuak94 authored Nov 14, 2019
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Commits on Nov 22, 2019

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

    …plit and maxOverlap for long reads.
    @joshuak94
    joshuak94 committed Nov 22, 2019
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Commits on Nov 25, 2019

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

    …nput.
    @joshuak94
    joshuak94 committed Nov 25, 2019
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  2. small fix

    @joshuak94
    joshuak94 committed Nov 25, 2019
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  3. Temporarily use origin/develop for sviper

    @joshuak94
    joshuak94 committed Nov 25, 2019
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  4. Introduce option to set thread count.

    @joshuak94
    joshuak94 committed Nov 25, 2019
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  5. More seqan namespace fixes.

    @joshuak94
    joshuak94 committed Nov 25, 2019
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Commits on Nov 26, 2019

  1. Print out maxSplitLong and maxOverlapLong, and make SViper toggleable

    @joshuak94
    joshuak94 committed Nov 26, 2019
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Commits on Nov 28, 2019

  1. Use UpdateBreakpoint instead of AddNewBreakpoint for combining short … 

    …and long reads.
    @joshuak94
    joshuak94 committed Nov 28, 2019
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  2. Only filter out SViper FAIL5 id.

    @joshuak94
    joshuak94 committed Nov 28, 2019
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Commits on Nov 29, 2019

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

    …lts are reported based on how confident the variant call is.
    @joshuak94
    joshuak94 committed Nov 29, 2019
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  2. Undo temporary checkout of SViper.

    @joshuak94
    joshuak94 committed Nov 29, 2019
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  3. Create another check on updating variant based on long read coverage.

    @joshuak94
    joshuak94 committed Nov 29, 2019
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  4. fix

    @joshuak94
    joshuak94 committed Nov 29, 2019
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  5. Move long read coverage to own function.

    @joshuak94
    joshuak94 committed Nov 29, 2019
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Commits on Dec 1, 2019

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

    @joshuak94
    joshuak94 committed Dec 1, 2019
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  2. Update sviper and print sviper header to log.

    @joshuak94
    joshuak94 committed Dec 1, 2019
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Commits on Dec 3, 2019

  1. update sviper

    @joshuak94
    joshuak94 committed Dec 3, 2019
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  2. update sviper

    @joshuak94
    joshuak94 committed Dec 3, 2019
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Commits on Feb 3, 2020

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

    … private member access.
    Joshua Kim committed Feb 3, 2020
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