Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / bcgsc/abyss issues and pull requests

#485 - ABySS singularity container on cluster issue

Issue - State: closed - Opened by zcalamari about 1 month ago - 3 comments

#484 - CI fixes

Pull Request - State: closed - Opened by lcoombe about 1 month ago

#100 - abyss-pe: make --mean the default method for DistanceEst when scaffolding

Issue - State: closed - Opened by benvvalk over 8 years ago - 4 comments
Labels: enhancement

#99 - Bug in abyss-scaffold when using abyss-longseqdist

Issue - State: closed - Opened by dbrowneup over 8 years ago - 16 comments
Labels: bug, stale

#98 - Sealer EXCEEDED_MEM_LIMIT error

Issue - State: closed - Opened by dbrowneup over 8 years ago - 4 comments

#97 - abyss-layout: Assertion `!get(vertex_removed, g, target(*e, g))' failed

Issue - State: closed - Opened by dbrowneup over 8 years ago - 5 comments
Labels: bug, wontfix

#96 - SAM Seq and Qual from abyss-map

Issue - State: closed - Opened by dbrowneup almost 9 years ago - 2 comments
Labels: question

#95 - Bugs in abyss-layout and abyss-filtergraph

Issue - State: closed - Opened by dbrowneup almost 9 years ago - 5 comments

#94 - Failed to create unitigs

Issue - State: closed - Opened by JETitus almost 9 years ago - 3 comments

#93 - Sealer requires read file arguments even when using a pre-built Bloom filter

Issue - State: closed - Opened by benvvalk almost 9 years ago - 3 comments
Labels: bug

#92 - abyss-pe has issue with bwa mem

Issue - State: closed - Opened by tnheider almost 9 years ago - 6 comments
Labels: question

#91 - Recipe for target '<name>' failed -- Fails while "generating adjacency?"

Issue - State: closed - Opened by mebbert almost 9 years ago - 11 comments

#90 - Sealer does not report Bloom filter FPR

Issue - State: closed - Opened by benvvalk almost 9 years ago - 2 comments
Labels: bug

#89 - Sealer does not implement -D option

Issue - State: closed - Opened by benvvalk about 9 years ago - 5 comments
Labels: bug, stale

#88 - Whole genome assembly using abyss-pe mpi

Issue - State: closed - Opened by Malabady about 9 years ago - 3 comments

#87 - abyss-dida: non-portable use of `readlink`

Issue - State: closed - Opened by benvvalk about 9 years ago - 1 comment
Labels: bug

#86 - Make sqlite3 an optional dependency

Issue - State: closed - Opened by benvvalk about 9 years ago - 2 comments
Labels: bug, stale

#85 - Error with Assertion `d.distance < 0' failed

Issue - State: closed - Opened by verne91 about 9 years ago - 29 comments
Labels: bug, stale

#84 - Error with Assertion `isalpha(seq[0])' failed

Issue - State: closed - Opened by verne91 about 9 years ago - 17 comments
Labels: question, stale

#83 - allow custom bwa mem options (e.g. "-x pacbio") during long-read scaffolding stage

Issue - State: closed - Opened by benvvalk about 9 years ago - 13 comments
Labels: enhancement, stale

#82 - rename abyss-sealer's --min-frag/--max-frag parameter

Issue - State: closed - Opened by benvvalk about 9 years ago - 1 comment
Labels: enhancement

#81 - Add PacBio scaffolding

Pull Request - State: closed - Opened by macmanes about 9 years ago - 5 comments
Labels: enhancement, stale

#80 - add in abyss-sealer to abyss-pe run

Pull Request - State: closed - Opened by macmanes about 9 years ago - 8 comments
Labels: enhancement, stale

#79 - abyss-sealer v1.9.0 fails to run to completion

Issue - State: closed - Opened by donovan-h-parks about 9 years ago - 8 comments
Labels: bug, stale

#78 - sort issue?

Issue - State: closed - Opened by macmanes over 9 years ago - 8 comments
Labels: invalid

#77 - Number of input files affects assembly speed

Issue - State: closed - Opened by damiankao over 9 years ago - 2 comments
Labels: enhancement, stale

#76 - use more portable /usr/bin/env perl for scripts

Pull Request - State: closed - Opened by wookietreiber over 9 years ago - 2 comments
Labels: bug

#75 - Invalid LICENSE file

Issue - State: closed - Opened by kblin over 9 years ago - 3 comments
Labels: question

#74 - abyss-bloom enhancements

Issue - State: closed - Opened by bschiffthaler over 9 years ago - 6 comments
Labels: enhancement

#73 - Documentation fixes.

Pull Request - State: closed - Opened by nsoranzo over 9 years ago - 20 comments
Labels: enhancement

#72 - Small fixes.

Pull Request - State: closed - Opened by nsoranzo over 9 years ago - 3 comments
Labels: enhancement

#71 - make check: undefined reference to `pthread_getspecific'

Issue - State: closed - Opened by sjackman over 9 years ago - 4 comments
Labels: build-error

#70 - Force abyss-pe to run with ABYSS instead of ABYSS-P

Issue - State: closed - Opened by yesimon over 9 years ago - 2 comments
Labels: question

#69 - some fixes for 32bit builds

Pull Request - State: closed - Opened by mcirsta over 9 years ago - 11 comments
Labels: build-error

#68 - compilation fails on i686 ( 32 bits )

Issue - State: closed - Opened by mcirsta over 9 years ago - 3 comments
Labels: build-error

#67 - error during make check, target common_stringutil

Issue - State: closed - Opened by wookietreiber over 9 years ago - 10 comments
Labels: build-error

#66 - Abyss crashes on aTRAM step

Issue - State: closed - Opened by daisieh over 9 years ago - 5 comments

#65 - Added "brew tap" command for OS X install.

Pull Request - State: closed - Opened by kubu4 over 9 years ago - 2 comments

#64 - Compilation error with icc / sparsehash-2.0.2

Issue - State: closed - Opened by prehensilecode almost 10 years ago - 13 comments
Labels: build-error, stale

#63 - command line errors

Issue - State: closed - Opened by zeeev almost 10 years ago

#62 - sparsehash error

Issue - State: closed - Opened by readmanchiu almost 10 years ago

#61 - subcommand gives incorrect version

Issue - State: closed - Opened by yannickwurm almost 10 years ago - 4 comments
Labels: enhancement, wontfix

#60 - Running ABySS on aarch64 machine

Issue - State: closed - Opened by ikitayama almost 10 years ago - 1 comment
Labels: enhancement

#59 - abyss-map crashes when a FASTA header matches the query better than the sequence

Issue - State: closed - Opened by ahammel about 10 years ago - 6 comments
Labels: bug, stale

#58 - DistanceEst missing options

Issue - State: closed - Opened by charmichaeld over 10 years ago - 1 comment
Labels: duplicate

#57 - DistanceEst missing options

Issue - State: closed - Opened by charmichaeld over 10 years ago - 9 comments
Labels: question

#56 - added support for fqzcomp

Pull Request - State: closed - Opened by aihardin over 10 years ago - 1 comment

#55 - errors when running abyss-pe

Issue - State: closed - Opened by binlangman over 10 years ago - 8 comments

#54 - Minor bug fix for 1.3.8

Pull Request - State: closed - Opened by ikitayama over 10 years ago - 7 comments

#53 - make: mixed implicit and normal rules

Issue - State: closed - Opened by sjackman over 10 years ago - 21 comments
Labels: bug

#52 - Include <string> for std::hash if FCC is used.

Pull Request - State: closed - Opened by ikitayama over 10 years ago - 7 comments

#51 - Add explicit version checking to autogen.sh

Pull Request - State: closed - Opened by ahammel over 10 years ago - 3 comments
Labels: build-error

#50 - Autconf complains of undefined macros

Issue - State: closed - Opened by ahammel over 10 years ago - 12 comments
Labels: build-error

#49 - Document ABySS file formats

Issue - State: closed - Opened by sjackman over 10 years ago - 9 comments
Labels: enhancement

#48 - AdjList: Bug involving invalidated pointers

Pull Request - State: closed - Opened by ikitayama almost 11 years ago - 5 comments
Labels: bug, build-error

#47 - PATCH for comping 1.3.7 with FCC

Issue - State: closed - Opened by ikitayama almost 11 years ago - 2 comments
Labels: bug, duplicate, build-error

#46 - Support reading CRAM data

Issue - State: closed - Opened by sjackman almost 11 years ago - 3 comments
Labels: enhancement, stale

#45 - Reduce FR/RF threshold for MP libraries

Issue - State: closed - Opened by sjackman almost 11 years ago - 1 comment

#44 - abyss-fixmate: std::unordered_map::erase can be slow

Issue - State: closed - Opened by sjackman almost 11 years ago - 2 comments

#43 - Error when SAM file contains @CO headers

Issue - State: closed - Opened by traymond almost 11 years ago - 1 comment
Labels: bug

#42 - Alignments are written to *.sam.gz instead of being piped to DistanceEst

Issue - State: closed - Opened by kmnip almost 11 years ago - 10 comments
Labels: bug, stale

#41 - Generate the stats file in multiple formats: tab-delimited, Markdown, HTML and CSV

Issue - State: closed - Opened by sjackman about 11 years ago - 3 comments
Labels: enhancement

#40 - error: use of overloaded operator '!=' is ambiguous

Issue - State: closed - Opened by sjackman about 11 years ago
Labels: build-error

#39 - error: call to 'cref' is ambiguous

Issue - State: closed - Opened by sjackman about 11 years ago
Labels: build-error

#38 - error: call to 'copy_if' is ambiguous

Issue - State: closed - Opened by sjackman about 11 years ago
Labels: build-error

#37 - error: implicit instantiation of undefined template 'std::__1::hash<cstring>'

Issue - State: closed - Opened by sjackman about 11 years ago - 1 comment
Labels: build-error

#36 - automake warning: the 'subdir-objects' automake option hasn't been enabled

Issue - State: closed - Opened by sjackman about 11 years ago - 1 comment
Labels: bug

#35 - error: no viable conversion from 'std::istream' (aka 'basic_istream<char>') to 'void *'

Issue - State: closed - Opened by sjackman about 11 years ago - 2 comments
Labels: build-error

#34 - abyss-fac: Add contig E-size

Issue - State: closed - Opened by sjackman about 11 years ago - 1 comment
Labels: enhancement

#33 - Dbgfm

Pull Request - State: closed - Opened by rchikhi about 11 years ago - 1 comment

#32 - KAligner fails to build with clang 5.0

Issue - State: closed - Opened by sjackman about 11 years ago - 2 comments
Labels: bug

#31 - Processing many files

Issue - State: closed - Opened by ikitayama about 11 years ago - 17 comments
Labels: bug

#30 - sam2afg: Skip secondary alignments

Issue - State: closed - Opened by sjackman about 11 years ago
Labels: enhancement

#29 - System.IO.MMap Error (abyss 1.3.6)

Issue - State: closed - Opened by bollig about 11 years ago - 4 comments
Labels: bug

#28 - AdjList produces incorrect adjacency info

Issue - State: closed - Opened by ikitayama about 11 years ago - 8 comments
Labels: bug

#27 - Downstream parallelization

Issue - State: closed - Opened by ikitayama about 11 years ago - 6 comments
Labels: enhancement, stale

#26 - error: typedef 'vertex_descriptor' locally defined but not used

Issue - State: closed - Opened by sjackman over 11 years ago - 9 comments
Labels: build-error

#25 - Assertion `it != m_edges.end()' failed.

Issue - State: closed - Opened by ikitayama over 11 years ago - 10 comments

#24 - Support mapping reads using BWA-mem

Issue - State: closed - Opened by sjackman over 11 years ago - 7 comments
Labels: enhancement

#23 - Control the log level through the -l option.

Pull Request - State: closed - Opened by ikitayama over 11 years ago - 5 comments
Labels: enhancement

#22 - Revert back old commit 0561dbc for non-gcc compilers

Pull Request - State: closed - Opened by ikitayama over 11 years ago - 15 comments
Labels: wontfix

#21 - AdjIO: Bug fix for non-GCC compilers

Pull Request - State: closed - Opened by ikitayama over 11 years ago - 9 comments
Labels: bug

#20 - ABYSS-P hangs at higher parallelism

Issue - State: closed - Opened by ikitayama over 11 years ago - 20 comments
Labels: question

#19 - Stats is different when ABYSS-P is used

Issue - State: closed - Opened by ikitayama over 11 years ago - 47 comments
Labels: bug

#18 - Use std::ios:off_type(0) together with std::ios::beg in seekg

Pull Request - State: closed - Opened by ikitayama over 11 years ago - 5 comments
Labels: bug

#17 - Fix program name (abyss-align -> abyss-mergepairs)

Pull Request - State: closed - Opened by eernst over 11 years ago - 1 comment
Labels: bug

#16 - DistanceEst error when no read pairs align to different contigs

Issue - State: closed - Opened by traymond almost 12 years ago - 1 comment
Labels: bug

#15 - abyss-samtobreak: automake error

Issue - State: closed - Opened by sjackman about 12 years ago
Labels: bug

#14 - abyss-map cannot handle multi-line fasta

Issue - State: closed - Opened by jts about 12 years ago - 4 comments
Labels: enhancement, stale

#13 - Fails to compile on OS X 10.8 Mountain Lion

Issue - State: closed - Opened by sjackman about 12 years ago - 2 comments
Labels: bug

#12 - Error running DistanceEst with Bowtie, Bowtie 2 and BWA

Issue - State: closed - Opened by traymond about 12 years ago - 5 comments
Labels: bug

#11 - ABYSS-P not exiting when file not found by bunzip2

Issue - State: closed - Opened by traymond about 12 years ago
Labels: bug

#10 - Abyss 1.3.4 and GCC 4.1 DistanceEst.cpp:141: aviso: convirtiendo a ‘int’ desde ‘double’:

Issue - State: closed - Opened by carojasq over 12 years ago - 2 comments
Labels: bug

#9 - Multi-line CASAVA-formatted FASTQ files are broken

Issue - State: closed - Opened by sjackman over 12 years ago
Labels: bug

#8 - SimpleGraph: extendPaths misassembles

Issue - State: closed - Opened by sjackman over 12 years ago
Labels: bug

#7 - Does not compile with GCC 4.7

Issue - State: closed - Opened by sjackman over 12 years ago
Labels: bug

#6 - MergePaths: Assertion failed: (!m_ambig)

Issue - State: closed - Opened by sjackman over 12 years ago - 1 comment
Labels: bug

#5 - scaffold.cc: warning: converting to unsigned int from double

Issue - State: closed - Opened by sjackman over 12 years ago - 1 comment
Labels: bug

#4 - abyss-map: error: Invalid argument

Issue - State: closed - Opened by sjackman over 12 years ago
Labels: bug

#3 - ParseAligns -l is broken

Issue - State: closed - Opened by sjackman over 12 years ago - 1 comment
Labels: bug