Ecosyste.ms: Issues

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

GitHub / gpertea/gffread issues and pull requests

#100 - empty output of cds.fa

Issue - State: open - Opened by Liyong-Zhang about 2 years ago - 1 comment

#100 - empty output of cds.fa

Issue - State: open - Opened by Liyong-Zhang about 2 years ago - 1 comment

#99 - Problem of overflow

Issue - State: open - Opened by thecgs about 2 years ago

#99 - Problem of overflow

Issue - State: open - Opened by thecgs about 2 years ago

#98 - gffread recognizes and converts

Issue - State: open - Opened by choiseungji over 2 years ago

#98 - gffread recognizes and converts

Issue - State: open - Opened by choiseungji over 2 years ago

#97 - option --nc not supported

Issue - State: closed - Opened by tbazilegith over 2 years ago - 5 comments

#97 - option --nc not supported

Issue - State: closed - Opened by tbazilegith over 2 years ago - 5 comments

#96 - Installation Failure

Issue - State: open - Opened by Botantisty over 2 years ago - 2 comments

#96 - Installation Failure

Issue - State: open - Opened by Botantisty over 2 years ago - 2 comments

#95 - Suggestion to support syntax for bcftools csq

Issue - State: open - Opened by lindenb over 2 years ago

#95 - Suggestion to support syntax for bcftools csq

Issue - State: open - Opened by lindenb over 2 years ago

#94 - Error: no genomic sequence available (check -g option!).

Issue - State: closed - Opened by raita27 over 2 years ago - 5 comments

#94 - Error: no genomic sequence available (check -g option!).

Issue - State: closed - Opened by raita27 over 2 years ago - 5 comments

#93 - make the defline of FASTA output more consistent

Issue - State: open - Opened by gpertea over 2 years ago
Labels: enhancement

#93 - make the defline of FASTA output more consistent

Issue - State: open - Opened by gpertea over 2 years ago
Labels: enhancement

#92 - Pathological CDS annotation classified as having no issues due to phase handling

Issue - State: open - Opened by nicolasrochette over 2 years ago
Labels: to investigate

#92 - Pathological CDS annotation classified as having no issues due to phase handling

Issue - State: open - Opened by nicolasrochette over 2 years ago
Labels: to investigate

#91 - GffObj::getSpliced() error: improper

Issue - State: open - Opened by abcdefghijklmn97 over 2 years ago - 2 comments

#91 - GffObj::getSpliced() error: improper

Issue - State: open - Opened by abcdefghijklmn97 over 2 years ago - 2 comments

#90 - output file only contains ENSEMBL gene ID and fasta sequence

Issue - State: open - Opened by thibui1996 over 2 years ago - 1 comment

#90 - output file only contains ENSEMBL gene ID and fasta sequence

Issue - State: open - Opened by thibui1996 over 2 years ago - 1 comment

#89 - From gtf to gff3

Issue - State: open - Opened by marco91sol almost 3 years ago

#89 - From gtf to gff3

Issue - State: open - Opened by marco91sol almost 3 years ago

#88 - Any way to keep the last stop codon results(*) when using -y option?

Issue - State: open - Opened by xiekunwhy almost 3 years ago - 1 comment

#88 - Any way to keep the last stop codon results(*) when using -y option?

Issue - State: open - Opened by xiekunwhy almost 3 years ago - 1 comment

#86 - Gene range inferred wrongly for pseudo-autosomal genes

Issue - State: open - Opened by hukai916 almost 3 years ago

#86 - Gene range inferred wrongly for pseudo-autosomal genes

Issue - State: open - Opened by hukai916 almost 3 years ago

#85 - Multiple Errors ---discarding overlapping duplicate gene feature

Issue - State: open - Opened by Liyong-Zhang almost 3 years ago - 2 comments

#85 - Multiple Errors ---discarding overlapping duplicate gene feature

Issue - State: open - Opened by Liyong-Zhang almost 3 years ago - 2 comments

#84 - handling for empty transcript_id

Issue - State: closed - Opened by murphyte almost 3 years ago - 5 comments

#84 - handling for empty transcript_id

Issue - State: closed - Opened by murphyte almost 3 years ago - 5 comments

#83 - Speed up of gffread

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

#83 - Speed up of gffread

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

#82 - unexpected Ns added to transcripts fasta

Issue - State: open - Opened by ramiroricardo about 3 years ago

#82 - unexpected Ns added to transcripts fasta

Issue - State: open - Opened by ramiroricardo about 3 years ago

#81 - Conversion from BED input uses "BED" as feature name

Issue - State: open - Opened by bernt-matthias about 3 years ago - 2 comments

#81 - Conversion from BED input uses "BED" as feature name

Issue - State: open - Opened by bernt-matthias about 3 years ago - 2 comments

#80 - Allow locus attribute on table output

Pull Request - State: open - Opened by ljyanesm about 3 years ago

#80 - Allow locus attribute on table output

Pull Request - State: open - Opened by ljyanesm about 3 years ago

#78 - shorter transcript not discarded using -K

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

#78 - shorter transcript not discarded using -K

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

#77 - Gffread extracts the wrong nucleotides from genome?

Issue - State: closed - Opened by stephanbitterwolf over 3 years ago - 1 comment

#77 - Gffread extracts the wrong nucleotides from genome?

Issue - State: closed - Opened by stephanbitterwolf over 3 years ago - 1 comment

#76 - Output issues for the -w, -x, and -y options

Issue - State: open - Opened by sjfleck over 3 years ago - 2 comments

#76 - Output issues for the -w, -x, and -y options

Issue - State: open - Opened by sjfleck over 3 years ago - 2 comments

#75 - cannot open input file (gff)

Issue - State: closed - Opened by Dongho1234 over 3 years ago

#75 - cannot open input file (gff)

Issue - State: closed - Opened by Dongho1234 over 3 years ago

#74 - GTF output file is different from GFF3 input file

Issue - State: open - Opened by eduardopdev over 3 years ago - 7 comments
Labels: to investigate

#74 - GTF output file is different from GFF3 input file

Issue - State: open - Opened by eduardopdev over 3 years ago - 7 comments
Labels: to investigate

#73 - Gzip support

Issue - State: open - Opened by starskyzheng over 3 years ago - 1 comment
Labels: enhancement

#73 - Gzip support

Issue - State: open - Opened by starskyzheng over 3 years ago - 1 comment
Labels: enhancement

#72 - Fix --version argument

Pull Request - State: closed - Opened by alephreish almost 4 years ago - 1 comment

#72 - Fix --version argument

Pull Request - State: closed - Opened by alephreish almost 4 years ago - 1 comment

#71 - -F does not write the features info

Issue - State: closed - Opened by husensofteng almost 4 years ago - 9 comments

#71 - -F does not write the features info

Issue - State: closed - Opened by husensofteng almost 4 years ago - 9 comments

#70 - Make -W (exon coordinates) argument work for -y (translations)

Pull Request - State: closed - Opened by alephreish almost 4 years ago

#70 - Make -W (exon coordinates) argument work for -y (translations)

Pull Request - State: closed - Opened by alephreish almost 4 years ago

#69 - remove duplicated lines

Pull Request - State: closed - Opened by Maarten-vd-Sande almost 4 years ago - 1 comment

#69 - remove duplicated lines

Pull Request - State: closed - Opened by Maarten-vd-Sande almost 4 years ago - 1 comment

#68 - Include GTF "transcript_version" attribute in .fa transcript name

Issue - State: closed - Opened by ACastanza almost 4 years ago - 10 comments
Labels: enhancement

#68 - Include GTF "transcript_version" attribute in .fa transcript name

Issue - State: closed - Opened by ACastanza almost 4 years ago - 10 comments
Labels: enhancement

#67 - gffread extracts wrong transcript sequence from reference FASTA

Issue - State: closed - Opened by LeonardoFurci about 4 years ago - 1 comment

#67 - gffread extracts wrong transcript sequence from reference FASTA

Issue - State: closed - Opened by LeonardoFurci about 4 years ago - 1 comment

#66 - Extract intron seq

Issue - State: open - Opened by bsb2014 about 4 years ago

#66 - Extract intron seq

Issue - State: open - Opened by bsb2014 about 4 years ago

#65 - CDS phase: -H has no effect

Issue - State: closed - Opened by alephreish about 4 years ago - 1 comment
Labels: bug

#65 - CDS phase: -H has no effect

Issue - State: closed - Opened by alephreish about 4 years ago - 1 comment
Labels: bug

#64 - empty files after running gffread with -x or -y

Issue - State: open - Opened by JonEilers about 4 years ago - 2 comments

#64 - empty files after running gffread with -x or -y

Issue - State: open - Opened by JonEilers about 4 years ago - 2 comments

#63 - gffread installation

Issue - State: closed - Opened by xiaolinchu92 about 4 years ago - 1 comment

#63 - gffread installation

Issue - State: closed - Opened by xiaolinchu92 about 4 years ago - 1 comment

#62 - Option to avoid adding StopCodon when converting GTF to GFF

Issue - State: open - Opened by estolle about 4 years ago

#62 - Option to avoid adding StopCodon when converting GTF to GFF

Issue - State: open - Opened by estolle about 4 years ago

#61 - Please send the version output to stdout and NOT stderr

Issue - State: open - Opened by Gaura about 4 years ago

#61 - Please send the version output to stdout and NOT stderr

Issue - State: open - Opened by Gaura about 4 years ago

#60 - build failure: GStrSet is not a template

Issue - State: closed - Opened by joelb123 about 4 years ago - 2 comments

#60 - build failure: GStrSet is not a template

Issue - State: closed - Opened by joelb123 about 4 years ago - 2 comments

#59 - gffread does not seem to use the .fai files it creates.

Issue - State: closed - Opened by NDHall about 4 years ago - 3 comments
Labels: bug

#59 - gffread does not seem to use the .fai files it creates.

Issue - State: closed - Opened by NDHall about 4 years ago - 3 comments
Labels: bug

#58 - Meaning of headline

Issue - State: open - Opened by biozhangzhou about 4 years ago

#58 - Meaning of headline

Issue - State: open - Opened by biozhangzhou about 4 years ago

#57 - Incorrect gene line and gene coordinates with options --keep-genes -C

Issue - State: open - Opened by gemygk about 4 years ago - 2 comments

#57 - Incorrect gene line and gene coordinates with options --keep-genes -C

Issue - State: open - Opened by gemygk about 4 years ago - 2 comments

#56 - Segfault when --keep-genes is combined with -C

Issue - State: closed - Opened by mrvollger over 4 years ago - 1 comment

#56 - Segfault when --keep-genes is combined with -C

Issue - State: closed - Opened by mrvollger over 4 years ago - 1 comment

#55 - Some genes lack 'exon' annotations after GFF3 to GTF conversion

Issue - State: closed - Opened by wflynny over 4 years ago - 2 comments

#55 - Some genes lack 'exon' annotations after GFF3 to GTF conversion

Issue - State: closed - Opened by wflynny over 4 years ago - 2 comments

#54 - GTF to GFF3: recover (or infer) gene feature

Issue - State: closed - Opened by LehmannN over 4 years ago - 7 comments
Labels: enhancement

#54 - GTF to GFF3: recover (or infer) gene feature

Issue - State: closed - Opened by LehmannN over 4 years ago - 7 comments
Labels: enhancement

#53 - citation for gffread

Issue - State: closed - Opened by fgypas over 4 years ago - 6 comments

#53 - citation for gffread

Issue - State: closed - Opened by fgypas over 4 years ago - 6 comments

#52 - extract cds sequence +- given bases

Issue - State: open - Opened by vivekbhr over 4 years ago - 1 comment
Labels: feature request

#52 - extract cds sequence +- given bases

Issue - State: open - Opened by vivekbhr over 4 years ago - 1 comment
Labels: feature request

#51 - Issue in reading CDS from GMAP-generated GFF3 file

Issue - State: open - Opened by pckorhon almost 5 years ago

#51 - Issue in reading CDS from GMAP-generated GFF3 file

Issue - State: open - Opened by pckorhon almost 5 years ago