Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Several changes #37

Open
wants to merge 60 commits into
base: develop_longread
Choose a base branch
from
Open

Several changes #37

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
60 commits
Select commit Hold shift + click to select a range
79d988b
Added seqan3 submodule
joshuak94 Oct 24, 2018
5304649
update seqan3 submodule
joshuak94 Jul 24, 2019
443819b
[INTERNAL] Adds seqan3 into the cmake files.
joshuak94 Oct 26, 2018
47a7825
switch hardcoded seqan with submodule
joshuak94 Aug 12, 2019
edea3e1
Merge pull request #1 from joshuak94/submodules
joshuak94 Aug 12, 2019
c06edc0
Phase in the argument_parser of seqan3 and replace completely the arg…
joshuak94 Oct 31, 2018
713c6a1
Terminate main program if any step returns false.
joshuak94 Nov 21, 2018
baeedec
fix seqan3::argument_parser bugs
joshuak94 Aug 12, 2019
23b42ff
Merge pull request #2 from joshuak94/arg_parser
joshuak94 Aug 12, 2019
6c3764e
Add option for long reads
joshuak94 Oct 8, 2019
45a5b83
Add seqan:: to everything.
joshuak94 Oct 10, 2019
2de9b0a
Merge pull request #3 from joshuak94/remove_namespace
joshuak94 Oct 10, 2019
bd3c733
Merge pull request #4 from joshuak94/long_read_input_only
joshuak94 Oct 10, 2019
8af9a10
Make the output file an option.
joshuak94 Oct 16, 2019
b4b0cea
Merge pull request #5 from joshuak94/option_fixes
joshuak94 Oct 16, 2019
8562348
Add SViper as a submodule. Update other submodules, update CMakeLists…
joshuak94 Oct 2, 2019
85f4543
Put calling of SViper commands into vaquita.cpp.
joshuak94 Oct 8, 2019
30aefa6
Introduce implicit conversion from VcfRecordEnhanced to Variant.
joshuak94 Oct 16, 2019
46d2c48
Prevent overwriting of info, quality and filter if they aren't empty.
joshuak94 Oct 16, 2019
de6bc16
Change the printing message to use seqan3:;debug_steram
joshuak94 Oct 8, 2019
a84da94
Allow alignment to choose between long and short reads
joshuak94 Oct 8, 2019
43ef35e
Beginning of long read integration
joshuak94 Oct 14, 2019
849ac40
Separate alignment and breakpoint managers into long and short reads.…
joshuak94 Nov 4, 2019
290bc0a
Enable merging of long read breakpoints into short read breakpoints.
joshuak94 Nov 6, 2019
6e01142
Create alignmentManager with boolean to indiciate if long or short re…
joshuak94 Nov 6, 2019
f9ce7b5
Change RUN_IF macro to set bool to true if condition not satisfied.
joshuak94 Nov 6, 2019
db70bdc
add null pointer check to pbamfileout
joshuak94 Nov 6, 2019
efa033e
Small fix to output of evidences found and fix to how breakpoints are…
joshuak94 Nov 6, 2019
03a95c0
Change from deleting lr breakpoints to just iterating to next one.
joshuak94 Nov 6, 2019
86dee99
Add check for breakpointmanager destructor to only delete splitread a…
joshuak94 Nov 7, 2019
724d1b7
Enable writing of breakpoint tsv.
joshuak94 Nov 7, 2019
fe21749
Add long read contig names if existing.
joshuak94 Nov 7, 2019
74dde81
Merge pull request #6 from joshuak94/sviper_variant_input
joshuak94 Nov 14, 2019
8a918f8
Merge pull request #7 from joshuak94/long_read
joshuak94 Nov 14, 2019
e061cca
Update SViper submodule. Change includes and namespace to reflect upd…
joshuak94 Nov 11, 2019
5ef8dd8
Fix how ref_chrom is set for the Variant object.
joshuak94 Nov 11, 2019
dc8dddc
Add SE definition to output header.
joshuak94 Nov 12, 2019
8d9cde2
Run SViper only if short and long reads are given.
joshuak94 Nov 12, 2019
4754143
Set skipped variants to pass.
joshuak94 Nov 13, 2019
e04f4cb
Add openmp to packages for compiling.
joshuak94 Nov 13, 2019
47b5edd
Merge pull request #8 from joshuak94/sviper_on_long_read
joshuak94 Nov 14, 2019
2e47376
Output sum of SE, CE, and PE when merging. Also create a default maxS…
joshuak94 Nov 22, 2019
9489bb6
Create default maxSplit and maxOverlap values specific to long read i…
joshuak94 Nov 21, 2019
ce9113e
small fix
joshuak94 Nov 21, 2019
b55c158
Temporarily use origin/develop for sviper
joshuak94 Nov 25, 2019
246d377
Introduce option to set thread count.
joshuak94 Nov 25, 2019
64febc8
More seqan namespace fixes.
joshuak94 Nov 25, 2019
682a881
Print out maxSplitLong and maxOverlapLong, and make SViper toggleable
joshuak94 Nov 26, 2019
626fb11
Use UpdateBreakpoint instead of AddNewBreakpoint for combining short …
joshuak94 Nov 28, 2019
3335db2
Only filter out SViper FAIL5 id.
joshuak94 Nov 28, 2019
3b5d834
Add more info to pass on to SViper, and switch how strict SViper resu…
joshuak94 Nov 29, 2019
d7652ea
Undo temporary checkout of SViper.
joshuak94 Nov 29, 2019
b30c062
Create another check on updating variant based on long read coverage.
joshuak94 Nov 29, 2019
06c0173
fix
joshuak94 Nov 29, 2019
5e81258
Move long read coverage to own function.
joshuak94 Nov 29, 2019
343fc21
Calculate short read length in Vaquita and pass on to SViper.
joshuak94 Dec 1, 2019
4471d67
Update sviper and print sviper header to log.
joshuak94 Dec 1, 2019
9ce02b0
update sviper
joshuak94 Dec 3, 2019
1a03584
update sviper
joshuak94 Dec 3, 2019
6813311
Update Seqan and Seqan3 submodules, update minimum CMake version, fix…
Feb 3, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
The table of contents is too big for display.
Diff view
Diff view
  •  
  •  
  •  
9 changes: 9 additions & 0 deletions .gitmodules
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
[submodule "seqan3"]
path = seqan3
url = [email protected]:seqan/seqan3.git
[submodule "seqan"]
path = seqan
url = [email protected]:seqan/seqan.git
[submodule "SViper"]
path = SViper
url = https://github.com/smehringer/SViper
8 changes: 4 additions & 4 deletions CMakeLists.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
project (vaquita CXX)
cmake_minimum_required (VERSION 3.0.0)
cmake_minimum_required (VERSION 3.4)

set (SEQAN_LIBRARY_PATH seqan-library-2.4.0)
set (SEQAN_LIBRARY_PATH seqan)
set (CMAKE_INCLUDE_PATH
${CMAKE_CURRENT_SOURCE_DIR}/${SEQAN_LIBRARY_PATH}/include/
${CMAKE_INCLUDE_PATH})
set (CMAKE_MODULE_PATH
${CMAKE_CURRENT_SOURCE_DIR}/${SEQAN_LIBRARY_PATH}/cmake/
${CMAKE_CURRENT_SOURCE_DIR}/${SEQAN_LIBRARY_PATH}/util/cmake/
${CMAKE_MODULE_PATH})
set (CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin/")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread -std=c++14 -O3 -DNDEBUG -DSEQAN_BGZF_NUM_THREAD=1")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread -std=c++17 -O3 -DNDEBUG -DSEQAN_BGZF_NUM_THREAD=1")

add_subdirectory(src)
1 change: 1 addition & 0 deletions SViper
Open in desktop
Submodule SViper added at 73761b
1 change: 1 addition & 0 deletions seqan
Open in desktop
Submodule seqan added at 5f3b6d
1 change: 0 additions & 1 deletion seqan-library-2.4.0/cmake/FindSeqAn.cmake
View file
Open in desktop

This file was deleted.

Loading