Ecosyste.ms: Issues

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

GitHub / bbuchfink/diamond issues and pull requests

#256 - Getting taxonomic output from Diamond

Issue - State: closed - Opened by jbatovska almost 6 years ago - 45 comments

#232 - --max-target-seqs: Issue or not with DIAMOND?

Issue - State: closed - Opened by MaryoHg about 6 years ago - 7 comments

#145 - Issue while running Diamond within Humann2

Issue - State: closed - Opened by bobems1215 over 7 years ago - 16 comments

#101 - Please provide manpage for diamond

Issue - State: open - Opened by tillea almost 8 years ago - 1 comment

#100 - Name space conflict with other diamond project

Issue - State: closed - Opened by tillea almost 8 years ago - 2 comments

#99 - option for filtering self-against-self hits?

Issue - State: closed - Opened by wdingx almost 8 years ago - 3 comments

#98 - issue on e_value reports

Issue - State: closed - Opened by wdingx almost 8 years ago - 8 comments

#97 - Error reading temporary file

Issue - State: closed - Opened by andreyurch almost 8 years ago - 6 comments

#96 - Adding an option for identity filtering?

Issue - State: closed - Opened by wdingx almost 8 years ago - 10 comments

#95 - Error: Invalid character (P/80) in sequence

Issue - State: closed - Opened by frcamacho almost 8 years ago - 5 comments

#94 - Error: Incompatible database version

Issue - State: closed - Opened by danshu about 8 years ago - 2 comments

#93 - diamond makedb: File format error: sequence of length 0

Issue - State: closed - Opened by moskalenko about 8 years ago - 4 comments

#92 - reported % identities are lower than those of BLASTX

Issue - State: closed - Opened by eead-csic-compbio about 8 years ago - 2 comments

#90 - runtime_error is not a member of std

Issue - State: closed - Opened by terrycojones about 8 years ago - 4 comments

#89 - Incorrect length of output sequences?

Issue - State: closed - Opened by terrycojones about 8 years ago - 2 comments

#88 - Error reading temporary file could be more informative

Issue - State: closed - Opened by terrycojones about 8 years ago - 1 comment

#87 - More information could be provided when throwing file_format_exception

Issue - State: closed - Opened by terrycojones about 8 years ago - 2 comments

#86 - Bizarre results

Issue - State: closed - Opened by pad1989 about 8 years ago - 3 comments

#85 - It would be good to be able to see gaps in the query and subject

Issue - State: closed - Opened by terrycojones about 8 years ago - 5 comments

#84 - SIGBUS when running diamond blastx on Mac OS X

Issue - State: closed - Opened by terrycojones about 8 years ago - 8 comments

#83 - qseq in outfmt 6 seems incorrect

Issue - State: closed - Opened by terrycojones about 8 years ago - 8 comments

#82 - It would be useful to be able to get the query title in output format 6

Issue - State: closed - Opened by terrycojones about 8 years ago - 3 comments

#81 - It would be useful to be able to get a database subject by title

Issue - State: closed - Opened by terrycojones about 8 years ago - 2 comments

#80 - diamond help should write to stdout not stderr

Issue - State: closed - Opened by terrycojones about 8 years ago - 2 comments

#79 - Anyone use diamond output xml file for b2gpipe?

Issue - State: open - Opened by ErisonChen about 8 years ago - 13 comments

#78 - --top not behaving as expected

Issue - State: closed - Opened by jwasmuth about 8 years ago - 2 comments

#77 - dmnd to fasta?

Issue - State: closed - Opened by aipolly about 8 years ago - 4 comments

#76 - Segmentation fault running blastx

Issue - State: closed - Opened by kennethban about 8 years ago - 14 comments

#75 - Remove -static to allow compilation on OSX

Pull Request - State: closed - Opened by wasade about 8 years ago

#74 - -static and OSX

Issue - State: closed - Opened by wasade about 8 years ago - 3 comments

#73 - Error: Error reading file diamond-57e3e9a9-1.tmp

Issue - State: closed - Opened by Lafond-LapalmeJ about 8 years ago - 7 comments

#72 - Unable to run blastx on block size > 2

Issue - State: closed - Opened by brymerr921 about 8 years ago - 5 comments

#71 - Fixed a bug that caused invalid XML files

Pull Request - State: closed - Opened by lucventurini about 8 years ago - 4 comments

#70 - Error while using view on daa file made with custom matrix

Issue - State: closed - Opened by mlirski about 8 years ago - 3 comments

#69 - Lambda and K for custom matrix

Issue - State: closed - Opened by cmerenstein about 8 years ago - 4 comments

#68 - compiling 0.8.18 from scratch

Issue - State: closed - Opened by Wildish-LBL about 8 years ago - 8 comments

#67 - Conversion of SAM to BAM using samtools.

Issue - State: open - Opened by twylie over 8 years ago - 11 comments

#66 - The result .m8 file!

Issue - State: closed - Opened by ErisonChen over 8 years ago - 6 comments

#65 - DIAMOND-windows needs C++ 2015

Issue - State: closed - Opened by DustinChen1986 over 8 years ago - 1 comment

#64 - Unable to process some files - segmentation fault

Issue - State: closed - Opened by brymerr921 over 8 years ago - 6 comments

#63 - Error running blastp file

Issue - State: closed - Opened by shravya-thatipally over 8 years ago - 8 comments

#62 - transcriptome annotation

Issue - State: closed - Opened by lmdu over 8 years ago - 1 comment

#61 - Package diamond using conda

Issue - State: closed - Opened by raphenya over 8 years ago - 2 comments
Labels: feature request

#60 - case of matrix parameter

Issue - State: closed - Opened by jvolkening over 8 years ago - 2 comments

#59 - Multiple sequences

Issue - State: closed - Opened by raphenya over 8 years ago - 2 comments

#58 - XML output

Issue - State: closed - Opened by raphenya over 8 years ago - 2 comments

#57 - diamond v0.8.14.76 - Segmentation fault: 11

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

#56 - Error while compiling from source diamond-0.8.14

Issue - State: closed - Opened by vagnerfonseca over 8 years ago - 3 comments

#55 - compliation issue introduced in 0.8.10

Issue - State: closed - Opened by Jehops over 8 years ago - 2 comments

#54 - Some edits to work with GCC 6.1 on Mac OS X:

Pull Request - State: closed - Opened by gaberoo over 8 years ago - 1 comment

#53 - Align multiple files

Issue - State: closed - Opened by jregalad over 8 years ago - 2 comments

#52 - Error version binary in windows

Issue - State: closed - Opened by vagnerfonseca over 8 years ago - 2 comments

#51 - Problems compiling version 0.8.7 on MacOS X

Issue - State: closed - Opened by ianpgm over 8 years ago - 2 comments

#50 - error with compiling v8.0.7 on Mac OSX

Issue - State: closed - Opened by Ewout1988 over 8 years ago - 2 comments

#49 - output format, what to do when xml is needed

Issue - State: closed - Opened by DHatziioanou over 8 years ago - 9 comments

#48 - Unaccounted Query Seqeunces

Issue - State: closed - Opened by adityabandla over 8 years ago - 7 comments

#47 - DIAMOND v0.8.5 ftell error

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

#46 - Diamond view reading gzipped files?

Issue - State: closed - Opened by dcdanko over 8 years ago - 7 comments
Labels: feature request

#45 - Error while compiling from source diamond-0.8.5

Issue - State: closed - Opened by VasilyTokarev over 8 years ago - 5 comments

#44 - Unexpectedly high memory usage

Issue - State: closed - Opened by donovan-h-parks over 8 years ago - 3 comments

#43 - FreeBSD package

Issue - State: closed - Opened by Jehops over 8 years ago - 3 comments

#42 - How to deliver the results to Blast2Go?

Issue - State: closed - Opened by DustinChen1986 over 8 years ago - 17 comments
Labels: feature request

#41 - Suggestions for Improving Diamond Output

Issue - State: closed - Opened by gemmahoad over 8 years ago - 2 comments

#40 - database naming issue .dmnd

Issue - State: closed - Opened by jjkoehorst over 8 years ago - 2 comments

#39 - a bug of blastx mode in v0.7.12?

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

#38 - Diamond threading behaves differently on similar systems...

Issue - State: closed - Opened by intendo over 8 years ago - 5 comments

#37 - Error diamond view

Issue - State: closed - Opened by agalychnica over 8 years ago - 1 comment

#36 - Enable "salltitles" option

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

#35 - Align the types of some options in main.cpp and options.h

Pull Request - State: closed - Opened by benfulton almost 9 years ago

#34 - how to set --band

Issue - State: closed - Opened by wmnwmn almost 9 years ago - 1 comment

#33 - Only return 1 when complaning about insufficient arguments

Pull Request - State: closed - Opened by kblin almost 9 years ago

#32 - cmake: Allow static builds of diamond

Pull Request - State: closed - Opened by kblin almost 9 years ago

#31 - (#13) Add a --version command line option

Pull Request - State: closed - Opened by kblin almost 9 years ago

#30 - Small file takes longer?

Issue - State: closed - Opened by wmnwmn almost 9 years ago - 1 comment

#29 - Question about max-target-seqs option

Issue - State: closed - Opened by wmnwmn almost 9 years ago - 15 comments

#28 - Segmentation fault: 11

Issue - State: closed - Opened by andreyurch almost 9 years ago - 17 comments

#27 - command line redirected input

Issue - State: closed - Opened by g1o almost 9 years ago - 1 comment

#26 - Feature request: blast "-outfmt 11 " output from diamond view

Issue - State: open - Opened by g1o almost 9 years ago - 4 comments
Labels: feature request

#25 - Invalid character (-/45) in sequence

Issue - State: closed - Opened by nekrut almost 9 years ago - 14 comments

#24 - pthread missing from CMakelists.txt

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

#23 - compilation problem

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

#22 - Options --matrix blosum45 and lower give "invalid scoring parameters"

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

#21 - Use BSD license

Pull Request - State: closed - Opened by colinbrislawn about 9 years ago

#20 - Different number of reads in input fasta and diamond results

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

#19 - Clarify license

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

#18 - On Linux, diamond is only for x86_64?

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

#16 - Return nonzero on usage error

Pull Request - State: closed - Opened by yunesj about 9 years ago

#15 - "Insufficient arguments" error should return nonzero exit status

Issue - State: closed - Opened by yunesj about 9 years ago

#14 - cmake build from source method not working

Issue - State: closed - Opened by wwood over 9 years ago

#13 - Add a --version flag

Issue - State: closed - Opened by tseemann over 9 years ago - 2 comments

#12 - Addresses Issue: https://github.com/bbuchfink/diamond/issues/11

Pull Request - State: closed - Opened by LeeBergstrand over 9 years ago - 1 comment

#10 - Ambiguous Nucleotides

Issue - State: closed - Opened by gedankenstuecke over 9 years ago - 4 comments

#9 - Input file is a DAA file (possibly related to issue - blastx error writing file)

Issue - State: closed - Opened by agrier04 over 9 years ago - 3 comments

#8 - blastx error writing file

Issue - State: open - Opened by agrier04 over 9 years ago - 5 comments

#7 - A few questions about the comparison between Diamond and BLASTX

Issue - State: closed - Opened by ilnamkang over 9 years ago - 1 comment

#6 - Default for query genetic code

Issue - State: closed - Opened by ilnamkang over 9 years ago - 7 comments
Labels: feature request

#5 - Command terminated abnormally error

Issue - State: closed - Opened by pcantalupo over 9 years ago - 10 comments

#4 - Error: Invalid character (@/64) in sequence

Issue - State: closed - Opened by lfaller over 9 years ago - 2 comments