marehr/dream_stellar issues and pull requests

#72 - Update runtime measurements for single threaded dream_stellar

Pull Request - State: closed - Opened by eaasna about 2 years ago

#71 - Search a single database segment determined by command line arguments

Pull Request - State: closed - Opened by eaasna about 2 years ago

#70 - Split option

Pull Request - State: closed - Opened by marehr over 2 years ago

#69 - Symlink gold standard

Pull Request - State: closed - Opened by marehr over 2 years ago

#68 - StellarApp::select_prefilter returns unique_ptr

Pull Request - State: closed - Opened by marehr over 2 years ago

#67 - Use database id map

Pull Request - State: closed - Opened by marehr over 2 years ago

#66 - Use query id map

Pull Request - State: closed - Opened by marehr over 2 years ago - 1 comment

#65 - Virtual prefilter

Pull Request - State: closed - Opened by marehr over 2 years ago

#64 - Refactor no query prefilter

Pull Request - State: closed - Opened by marehr over 2 years ago

#63 - stellar.main.tpp: split out parallel_prefilter

Pull Request - State: closed - Opened by marehr over 2 years ago

#62 - stellar.main.tpp: split out parallel_prefilter

Pull Request - State: closed - Opened by marehr over 2 years ago

#61 - stellar.main.tpp: Split out search_and_verify

Pull Request - State: closed - Opened by marehr over 2 years ago

#60 - stellar::SwiftHitVerifier use stellar::EPSMatchOptions + stellar::Ver…

Pull Request - State: closed - Opened by marehr over 2 years ago - 1 comment

#59 - stellar::StellarIndex::{qgramIndexFromPattern, sequencesFromPattern, …

Pull Request - State: closed - Opened by marehr over 2 years ago

#58 - Move seqan::Cargo definition into stellar::StellarIndex

Pull Request - State: closed - Opened by marehr over 2 years ago

#57 - Split options

Pull Request - State: closed - Opened by marehr over 2 years ago

#56 - [NOP] Simplify SwiftHitVerifier

Pull Request - State: closed - Opened by marehr over 2 years ago

#55 - [FIX] DatabaseIDMap use more specific header and prefix seqan code

Pull Request - State: closed - Opened by marehr over 2 years ago

#54 - [FIX] StellarIndex can't be moved or copied

Pull Request - State: closed - Opened by marehr over 2 years ago

#53 - Index of line segments

Pull Request - State: closed - Opened by marehr over 2 years ago

#52 - Renaming vars

Pull Request - State: closed - Opened by marehr over 2 years ago

#51 - Inner timing

Pull Request - State: closed - Opened by marehr over 2 years ago

#50 - Whitespace changes

Pull Request - State: closed - Opened by marehr over 2 years ago

#49 - Add more detailed timing information

Pull Request - State: closed - Opened by marehr over 2 years ago

#48 - Write files outside

Pull Request - State: closed - Opened by marehr over 2 years ago

#47 - Nsegment database split

Pull Request - State: closed - Opened by marehr over 2 years ago

#46 - Add test for longestEpsMatch

Pull Request - State: closed - Opened by marehr over 2 years ago

#45 - test: add alignment_fragment class

Pull Request - State: closed - Opened by marehr over 2 years ago

#44 - No query prefilter no split

Pull Request - State: closed - Opened by marehr over 2 years ago

#43 - Revert change

Pull Request - State: closed - Opened by marehr over 2 years ago

#42 - Align banded nw best ends

Pull Request - State: closed - Opened by marehr over 2 years ago

#41 - Use fraction

Pull Request - State: closed - Opened by marehr over 2 years ago

#40 - Simplify stellar statistics

Pull Request - State: closed - Opened by marehr over 2 years ago

#39 - Test verification

Pull Request - State: closed - Opened by marehr over 2 years ago

#38 - Deterministic output

Pull Request - State: closed - Opened by marehr over 2 years ago

#37 - StellarIndex: use _stellarKernel

Pull Request - State: closed - Opened by marehr over 2 years ago

#36 - SwiftHitVerifier: accept Stellar(Database|Query)Segment

Pull Request - State: closed - Opened by marehr over 2 years ago

#35 - After Fixing the UB, we can now simplify copying the left extension.

Pull Request - State: closed - Opened by marehr over 2 years ago

#34 - FIX UB: use scoring scheme directly

Pull Request - State: closed - Opened by marehr almost 3 years ago

#33 - Split extension

Pull Request - State: closed - Opened by marehr almost 3 years ago - 1 comment

#32 - Use InfixSegment in StellarSwiftFinder instead of String (and add test)

Pull Request - State: closed - Opened by marehr almost 3 years ago

#31 - Stellar sequence segment

Pull Request - State: closed - Opened by marehr almost 3 years ago

#30 - Major: pass onAlignmentResult callback instead of explicit querymatches.

Pull Request - State: closed - Opened by marehr almost 3 years ago

#29 - Pull out diagnostics

Pull Request - State: closed - Opened by marehr almost 3 years ago

#28 - Pull out verification code from stellar.hpp

Pull Request - State: closed - Opened by marehr about 3 years ago

#27 - Make verificationMethod a "std::variant"

Pull Request - State: closed - Opened by marehr about 3 years ago

#26 - Move header

Pull Request - State: closed - Opened by marehr about 3 years ago

#25 - Update app template

Pull Request - State: closed - Opened by marehr about 3 years ago

#24 - Masterplan for dream-stellar

Issue - State: open - Opened by marehr about 3 years ago - 1 comment

#23 - Parallize

Pull Request - State: closed - Opened by marehr about 3 years ago

#22 - Small restructure

Pull Request - State: closed - Opened by marehr about 3 years ago

#21 - Split loop for forward and reverse calculation

Pull Request - State: closed - Opened by marehr about 3 years ago

#20 - add tests for multipe databases and queries

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#19 - Add more test2

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#18 - Use whitespace instead of ascii code

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#17 - Separate statistics

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#16 - Dry output matches

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#15 - More modular

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#14 - Use namespace stellar and stellar::app

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#13 - app template: remove unused files

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#12 - cmake: add options to allow multiple translation units and PCH

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#11 - Const database and query

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#10 - [FIX] copy sequences locally on left sequence extensions

Pull Request - State: closed - Opened by marehr about 3 years ago

#9 - Copy infix alignment into alignment

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#8 - Make underlying Sequence const for Segments

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#8 - Make underlying Sequence const for Segments

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#7 - Move out infix

Pull Request - State: closed - Opened by marehr about 3 years ago

#6 - Move out diagonal

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#5 - Make many things const if they can.

Pull Request - State: closed - Opened by marehr about 3 years ago

#4 - Add parallel mode to stellar

Issue - State: closed - Opened by marehr about 3 years ago

#3 - Untabify source code

Pull Request - State: closed - Opened by marehr about 3 years ago

#2 - Code refactoring

Pull Request - State: closed - Opened by marehr about 3 years ago - 1 comment

#1 - More tests

Pull Request - State: closed - Opened by marehr about 3 years ago

GitHub / marehr/dream_stellar issues and pull requests