Steffen Möller pushed to branch master at Debian Med / gffread
Commits: 2148d2d5 by Steffen Moeller at 2020-01-27T11:04:01+01:00 New upstream version 0.11.7 - - - - - 62bc6ef9 by Steffen Moeller at 2020-01-27T11:04:01+01:00 routine-update: New upstream version - - - - - ec93359d by Steffen Moeller at 2020-01-27T11:04:02+01:00 Update upstream source from tag 'upstream/0.11.7' Update to upstream version '0.11.7' with Debian dir 142edcb67e02a319ba5a9881eca1330e498f1b7f - - - - - 53df8efd by Steffen Moeller at 2020-01-27T11:04:16+01:00 routine-update: Ready to upload to unstable - - - - - af549ae2 by Steffen Moeller at 2020-01-27T11:06:03+01:00 Updated standard to 4.5.0 - - - - - 3 changed files: - debian/changelog - debian/control - gffread.cpp Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +gffread (0.11.7-1) unstable; urgency=medium + + * Team upload. + * New upstream version + * Standards-Version: 4.5.0 + + -- Steffen Moeller <[email protected]> Mon, 27 Jan 2020 11:04:06 +0100 + gffread (0.11.6-1) unstable; urgency=medium * Another test exemption from rtracklayer ===================================== debian/control ===================================== @@ -5,8 +5,8 @@ Uploaders: Andreas Tille <[email protected]>, Section: science Priority: optional Build-Depends: debhelper-compat (= 12), - libgclib-dev (>= 0.11.3) -Standards-Version: 4.4.0 + libgclib-dev +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/gffread Vcs-Git: https://salsa.debian.org/med-team/gffread.git Homepage: https://github.com/gpertea/gffread ===================================== gffread.cpp ===================================== @@ -4,7 +4,7 @@ #define __STDC_FORMAT_MACROS #include <inttypes.h> -#define VERSION "0.11.6" +#define VERSION "0.11.7" #define USAGE "gffread v" VERSION ". Usage:\n\ gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>] \n\ @@ -126,7 +126,8 @@ Output options:\n\ --table output a simple tab delimited format instead of GFF, with columns\n\ having the values of GFF attributes given in <attrlist>; special\n\ pseudo-attributes (prefixed by @) are recognized:\n\ - @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen\n\ + @id, @geneid, @chr, @start, @end, @strand, @numexons, @exons, \n\ + @cds, @covlen, @cdslen\n\ -v,-E expose (warn about) duplicate transcript IDs and other potential\n\ problems with the given GFF/GTF records\n\ " @@ -159,7 +160,8 @@ class RefTran { enum ETableFieldType { ctfGFF_Attr=0, // attribute name as is - ctfGFF_ID, //ID or @id + ctfGFF_ID, //ID or @id or transcript_id + ctfGFF_geneID, //geneID or @gene_id ctfGFF_Parent, //Parent or @parent ctfGFF_chr, //@chr ctfGFF_feature, //@feature @@ -293,6 +295,7 @@ void setTableFormat(GStr& s) { GHash<ETableFieldType> specialFields; specialFields.Add("chr", new ETableFieldType(ctfGFF_chr)); specialFields.Add("id", new ETableFieldType(ctfGFF_ID)); + specialFields.Add("geneid", new ETableFieldType(ctfGFF_geneID)); specialFields.Add("parent", new ETableFieldType(ctfGFF_Parent)); specialFields.Add("feature", new ETableFieldType(ctfGFF_feature)); specialFields.Add("start", new ETableFieldType(ctfGFF_start)); @@ -317,11 +320,16 @@ void setTableFormat(GStr& s) { else GMessage("Warning: table field '@%s' not recognized!\n",w.chars()); continue; } - if (w=="ID") { + if (w=="ID" || w=="transcript_id") { CTableField tcol(ctfGFF_ID); tableCols.Add(tcol); continue; } + if (w=="geneID" || w=="gene_id") { + CTableField tcol(ctfGFF_geneID); + tableCols.Add(tcol); + continue; + } if (w=="Parent") { CTableField tcol(ctfGFF_Parent); tableCols.Add(tcol); @@ -951,6 +959,9 @@ void printGxfTab(FILE* f, GffObj& g) { case ctfGFF_ID: fprintf(f,"%s",g.getID()); break; + case ctfGFF_geneID: + fprintf(f,"%s",g.getGeneID()); + break; case ctfGFF_Parent: if (g.parent!=NULL) fprintf(f,"%s",g.parent->getID()); else fprintf(f, "."); View it on GitLab: https://salsa.debian.org/med-team/gffread/compare/b60ce1c38c7c8ccf1789182acf11d473b9ffbcbd...af549ae20de8b5df5bf1d5bb0bf76aeb68186d70 -- View it on GitLab: https://salsa.debian.org/med-team/gffread/compare/b60ce1c38c7c8ccf1789182acf11d473b9ffbcbd...af549ae20de8b5df5bf1d5bb0bf76aeb68186d70 You're receiving this email because of your account on salsa.debian.org.
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