seqan/seqan issues and pull requests

#2535 - [INFRA] Add clang-19

Pull Request - State: closed - Opened by eseiler 11 days ago

#2534 - Mason simulator - generate error free illumina reads

Issue - State: open - Opened by mariaelf97 24 days ago - 1 comment

#2533 - Mason Simulator Segmentation fault

Issue - State: open - Opened by rvarki about 1 month ago

#2532 - Check k-mer counts

Pull Request - State: closed - Opened by eaasna 2 months ago

#2531 - [INFRA] Fix Sanitizer

Pull Request - State: closed - Opened by eseiler 3 months ago

#2530 - [INFRA] Remove SEQAN_GH_ACTIONS_BUILD

Pull Request - State: closed - Opened by eseiler 4 months ago

#2529 - [FIX] heap-use-after-free

Pull Request - State: closed - Opened by eseiler 4 months ago

#2528 - [FIX] heap-use-after-free

Pull Request - State: closed - Opened by eseiler 4 months ago

#2527 - [INFRA] Apply Debian patches

Pull Request - State: closed - Opened by eseiler 4 months ago

#2526 - [FIX,INFRA] Sanitizer builds

Pull Request - State: closed - Opened by eseiler 4 months ago

#2525 - [FIX] Segfault in GlobalAlignment

Pull Request - State: closed - Opened by eseiler 4 months ago

#2524 - Unallocated memory read which causes occasional segment faults during banded alignments

Issue - State: closed - Opened by paoloshasta 4 months ago - 1 comment

#2523 - [INFRA] Update CI

Pull Request - State: closed - Opened by eseiler 4 months ago

#2522 - [MISC] Expand gcc workaround

Pull Request - State: closed - Opened by eseiler 5 months ago

#2521 - [FIX] mason

Pull Request - State: closed - Opened by eseiler 5 months ago

#2520 - mason2 assertion failures

Issue - State: closed - Opened by marcelm 5 months ago - 14 comments

#2518 - Job getting killed without a error message

Issue - State: closed - Opened by vinegang 7 months ago - 3 comments

#2517 - Error occured while running mason simulator

Issue - State: closed - Opened by sahilrishav2 7 months ago - 1 comment

#2516 - (Uncaught exception of type std::runtime_error: Illumina read is too long, increase fragment length)

Issue - State: closed - Opened by mariaelf97 8 months ago - 2 comments

#2515 - [FIX] Missing SQ header in BAM output

Pull Request - State: closed - Opened by eseiler 8 months ago

#2514 - [FIX] mason_variator: Fix StructuralVariantRecord::endPosition() for deletions.

Pull Request - State: closed - Opened by smehringer 8 months ago - 2 comments

#2513 - yara_mapper: Assertion failed : length(me.cigar) <= length(me.cigarSet[matchId])

Issue - State: closed - Opened by jhu99 8 months ago - 3 comments

#2512 - question about parallel alignment of different seqence

Issue - State: closed - Opened by metaphysicser 9 months ago - 2 comments

#2511 - mason_variator Aborted (core dumped)

Issue - State: closed - Opened by amiliehj 9 months ago - 1 comment

#2510 - [DOC] Update Changelog, Readme, and links

Pull Request - State: closed - Opened by eseiler 10 months ago

#2509 - [DOC] Update changelog

Pull Request - State: closed - Opened by eseiler 10 months ago

#2508 - [DOC] Add caveats section for mason

Pull Request - State: closed - Opened by eseiler 10 months ago

#2507 - [FIX] CMake: Use execute_process

Pull Request - State: closed - Opened by eseiler 10 months ago

#2506 - [MISC] Update copyright year

Pull Request - State: closed - Opened by eseiler 10 months ago

#2505 - mason_simulator error: (Uncaught exception of type MasonIOException: Could not build FAI index.)

Issue - State: closed - Opened by cwatt 10 months ago - 6 comments

#2504 - Bump actions/setup-python from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago
Labels: dependencies

#2503 - Bump conda-incubator/setup-miniconda from 2 to 3

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago
Labels: dependencies

#2502 - [INFRA] Update CI

Pull Request - State: closed - Opened by eseiler about 1 year ago

#2501 - [INFRA] Fix CMake warnings

Pull Request - State: closed - Opened by eseiler about 1 year ago

#2500 - Bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#2499 - README.md with dead links

Issue - State: closed - Opened by Austernpilz over 1 year ago - 2 comments

#2498 - [INFRA] Simplify find package, add seqan::seqan2

Pull Request - State: closed - Opened by eseiler over 1 year ago

#2497 - [INFRA] Rename namespace to seqan2

Pull Request - State: closed - Opened by eseiler over 1 year ago

#2496 - [DOC] master/develop -> main

Pull Request - State: closed - Opened by eseiler over 1 year ago

#2495 - Bump actions/setup-python from 2 to 4

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#2494 - Bump Pendect/action-rsyncer from 1.1.0 to 2.0.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#2493 - [MISC] Merge develop into main

Pull Request - State: closed - Opened by eseiler over 1 year ago

#2492 - fix: rename master to main

Pull Request - State: closed - Opened by SGSSGene over 1 year ago

#2491 - Doc/adjust readme and compilers

Pull Request - State: closed - Opened by SGSSGene over 1 year ago - 1 comment

#2490 - mason_simulator Segmentation fault (core dumped)

Issue - State: closed - Opened by MarcelloMalpighi over 1 year ago - 12 comments

#2489 - Question: is it possible to create a psl like output from razers3 ?

Issue - State: closed - Opened by Aphrix almost 2 years ago - 2 comments

#2488 - [INFRA] dddoc

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

#2487 - BUG: simulation might produce 'N' even this is not intended

Issue - State: open - Opened by SGSSGene about 2 years ago - 1 comment
Labels: bug

#2486 - Incorrect number reported in "XS:i:", when using mason_simulate to simulate variants and reads.

Issue - State: closed - Opened by Lilu-guo about 2 years ago - 9 comments

#2485 - Lets see what happens if we remove this weird define

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

#2484 - [FIX] vcf writter wrote out the wrong information

Pull Request - State: open - Opened by SGSSGene over 2 years ago

#2483 - [FIX] add missing definition of static variables

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

#2482 - [DOC] Add documentation on mason2 file handle problem.

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

#2481 - [FIX] FMIndex/approximate using short search schemes

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

#2480 - [INFRA] CI: harden compiler flags

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

#2479 - [INFRA] Update CI

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

#2478 - [FIX] gcc12: maybe unitialised

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

#2477 - [FIX] -Waddress

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

#2476 - [FIX] mason2 vcf parsing

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

#2475 - Error Mason2 parsing VCF file v4.2 with multiple formats in the `FORMAT` field

Issue - State: closed - Opened by maxrossi91 almost 3 years ago - 10 comments