[med-svn] [Git][med-team/libgff][master] 6 commits: Add autopkgtests
Nilesh Patra
gitlab at salsa.debian.org
Tue Jun 2 18:18:06 BST 2020
Nilesh Patra pushed to branch master at Debian Med / libgff
Commits:
173e88ca by Nilesh Patra at 2020-06-02T22:32:47+05:30
Add autopkgtests
- - - - -
1ba845d8 by Nilesh Patra at 2020-06-02T22:33:01+05:30
Install relevant examples
- - - - -
95203892 by Nilesh Patra at 2020-06-02T17:05:17+00:00
Fix with cme
- - - - -
ae20f328 by Nilesh Patra at 2020-06-02T17:05:59+00:00
Add upstream/metadata
- - - - -
3410ac12 by Nilesh Patra at 2020-06-02T22:36:59+05:30
Fix white space
- - - - -
b9285521 by Nilesh Patra at 2020-06-02T22:43:10+05:30
Fix file permissions and trailing white spaces
- - - - -
10 changed files:
- − debian/compat
- debian/control
- debian/copyright
- + debian/examples
- debian/rules
- + debian/tests/README
- + debian/tests/control
- + debian/tests/data/example.gtf
- + debian/tests/run-unit-test
- + debian/upstream/metadata
Changes:
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,12 +3,13 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>
Section: libdevel
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 13),
cmake
-Standards-Version: 4.1.4
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/libgff
Vcs-Git: https://salsa.debian.org/med-team/libgff.git
Homepage: https://github.com/Kingsford-Group/libgff
+Rules-Requires-Root: no
Package: libgff-dev
Architecture: any
@@ -19,4 +20,4 @@ Description: GFF/GTF parsing from cufflinks as a library
the Cufflinks codebase. There are not many (any?) relatively lightweight
GTF/GFF parsers exposing a C++ interface, and the goal of this library is to
provide this functionality without the necessity of drawing in a heavy-weight
- dependency like SeqAn.
+ dependency like SeqAn.
=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: libgff
Source: https://github.com/Kingsford-Group/libgff
@@ -34,5 +34,3 @@ License: BSL-1.0
FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
-
-
=====================================
debian/examples
=====================================
@@ -0,0 +1,2 @@
+src/TestGFFParse.cpp
+debian/tests/data/*
=====================================
debian/rules
=====================================
@@ -5,3 +5,6 @@
%:
dh $@
+override_dh_fixperms:
+ dh_fixperms
+ find debian -name '*.gtf' | xargs chmod -x
=====================================
debian/tests/README
=====================================
@@ -0,0 +1,5 @@
+Tests for libgff
+=================
+
+The debian/tests/data/* has been referenced from:
+ https://www.icgeb.org/
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,4 @@
+Tests: run-unit-test
+Depends: @, python-pysam-tests
+Restrictions: allow-stderr
+
=====================================
debian/tests/data/example.gtf
=====================================
@@ -0,0 +1,52 @@
+NC_000024.9 RefSeq gene 120310 122812 . + . gene_id "NC_000024.9:NCRNA00108"; gene_synonym "CXYorf11"; note "Derived by automated computational analysis using gene prediction method: Curated Genomic."; pseudo ""; db_xref "GeneID:677739"; db_xref "HGNC:31847";
+NC_000024.9 RefSeq gene 142991 170020 . + . gene_id "NC_000024.9:PLCXD1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; db_xref "GeneID:55344"; db_xref "HGNC:23148";
+NC_000024.9 RefSeq exon 142991 143061 . + . gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; gbkey "mRNA"; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_018390.2"; db_xref "GeneID:55344"; db_xref "GI:94158612"; exon_number "1";
+NC_000024.9 RefSeq exon 148149 148351 . + . gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; gbkey "mRNA"; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_018390.2"; db_xref "GeneID:55344"; db_xref "GI:94158612"; exon_number "2";
+NC_000024.9 RefSeq exon 150834 150981 . + . gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; gbkey "mRNA"; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_018390.2"; db_xref "GeneID:55344"; db_xref "GI:94158612"; exon_number "3";
+NC_000024.9 RefSeq exon 155400 155536 . + . gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; gbkey "mRNA"; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_018390.2"; db_xref "GeneID:55344"; db_xref "GI:94158612"; exon_number "4";
+NC_000024.9 RefSeq exon 157315 157443 . + . gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; gbkey "mRNA"; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_018390.2"; db_xref "GeneID:55344"; db_xref "GI:94158612"; exon_number "5";
+NC_000024.9 RefSeq exon 158166 158321 . + . gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; gbkey "mRNA"; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_018390.2"; db_xref "GeneID:55344"; db_xref "GI:94158612"; exon_number "6";
+NC_000024.9 RefSeq exon 159702 159885 . + . gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; gbkey "mRNA"; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_018390.2"; db_xref "GeneID:55344"; db_xref "GI:94158612"; exon_number "7";
+NC_000024.9 RefSeq exon 165764 166059 . + . gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; gbkey "mRNA"; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_018390.2"; db_xref "GeneID:55344"; db_xref "GI:94158612"; exon_number "8";
+NC_000024.9 RefSeq exon 169260 170020 . + . gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; gbkey "mRNA"; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_018390.2"; db_xref "GeneID:55344"; db_xref "GI:94158612"; exon_number "9";
+NC_000024.9 RefSeq CDS 150855 150981 . + 0 gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; protein_id "NP_060860.1"; db_xref "CCDS:CCDS14103.1"; db_xref "GeneID:55344"; db_xref "GI:8922995"; exon_number "1";
+NC_000024.9 RefSeq CDS 155400 155536 . + 2 gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; protein_id "NP_060860.1"; db_xref "CCDS:CCDS14103.1"; db_xref "GeneID:55344"; db_xref "GI:8922995"; exon_number "2";
+NC_000024.9 RefSeq CDS 157315 157443 . + 0 gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; protein_id "NP_060860.1"; db_xref "CCDS:CCDS14103.1"; db_xref "GeneID:55344"; db_xref "GI:8922995"; exon_number "3";
+NC_000024.9 RefSeq CDS 158166 158321 . + 0 gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; protein_id "NP_060860.1"; db_xref "CCDS:CCDS14103.1"; db_xref "GeneID:55344"; db_xref "GI:8922995"; exon_number "4";
+NC_000024.9 RefSeq CDS 159702 159885 . + 0 gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; protein_id "NP_060860.1"; db_xref "CCDS:CCDS14103.1"; db_xref "GeneID:55344"; db_xref "GI:8922995"; exon_number "5";
+NC_000024.9 RefSeq CDS 165764 165999 . + 2 gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; protein_id "NP_060860.1"; db_xref "CCDS:CCDS14103.1"; db_xref "GeneID:55344"; db_xref "GI:8922995"; exon_number "6";
+NC_000024.9 RefSeq start_codon 150855 150857 . + 0 gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; protein_id "NP_060860.1"; db_xref "CCDS:CCDS14103.1"; db_xref "GeneID:55344"; db_xref "GI:8922995"; exon_number "1";
+NC_000024.9 RefSeq stop_codon 166000 166002 . + 0 gene_id "NC_000024.9:PLCXD1"; transcript_id "NM_018390.2"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; product "phosphatidylinositol-specific phospholipase C, X domain containing 1"; protein_id "NP_060860.1"; db_xref "CCDS:CCDS14103.1"; db_xref "GeneID:55344"; db_xref "GI:8922995"; exon_number "1";
+NC_000024.9 RefSeq gene 171426 180887 . - . gene_id "NC_000024.9:GTPBP6"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; db_xref "GeneID:8225"; db_xref "HGNC:30189"; db_xref "MIM:300124";
+NC_000024.9 RefSeq exon 180817 180887 . - . gene_id "NC_000024.9:GTPBP6"; transcript_id "NM_012227.1"; gbkey "mRNA"; product "GTP binding protein 6 (putative)"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; exception "unclassified transcription discrepancy"; insd_transcript_id "NM_012227.1"; db_xref "GeneID:8225"; db_xref "GI:6912587"; exon_number "1";
+NC_000024.9 RefSeq exon 179433 179591 . - . gene_id "NC_000024.9:GTPBP6"; transcript_id "NM_012227.1"; gbkey "mRNA"; product "GTP binding protein 6 (putative)"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; exception "unclassified transcription discrepancy"; insd_transcript_id "NM_012227.1"; db_xref "GeneID:8225"; db_xref "GI:6912587"; exon_number "2";
+NC_000024.9 RefSeq exon 178086 178294 . - . gene_id "NC_000024.9:GTPBP6"; transcript_id "NM_012227.1"; gbkey "mRNA"; product "GTP binding protein 6 (putative)"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; exception "unclassified transcription discrepancy"; insd_transcript_id "NM_012227.1"; db_xref "GeneID:8225"; db_xref "GI:6912587"; exon_number "3";
+NC_000024.9 RefSeq exon 174399 174547 . - . gene_id "NC_000024.9:GTPBP6"; transcript_id "NM_012227.1"; gbkey "mRNA"; product "GTP binding protein 6 (putative)"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; exception "unclassified transcription discrepancy"; insd_transcript_id "NM_012227.1"; db_xref "GeneID:8225"; db_xref "GI:6912587"; exon_number "4";
+NC_000024.9 RefSeq exon 174027 174179 . - . gene_id "NC_000024.9:GTPBP6"; transcript_id "NM_012227.1"; gbkey "mRNA"; product "GTP binding protein 6 (putative)"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; exception "unclassified transcription discrepancy"; insd_transcript_id "NM_012227.1"; db_xref "GeneID:8225"; db_xref "GI:6912587"; exon_number "5";
+NC_000024.9 RefSeq exon 171426 171864 . - . gene_id "NC_000024.9:GTPBP6"; transcript_id "NM_012227.1"; gbkey "mRNA"; product "GTP binding protein 6 (putative)"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; exception "unclassified transcription discrepancy"; insd_transcript_id "NM_012227.1"; db_xref "GeneID:8225"; db_xref "GI:6912587"; exon_number "6";
+NC_000024.9 RefSeq CDS 180817 180887 . - 0 gene_id "NC_000024.9:GTPBP6"; transcript_id "NM_012227.1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; exception "unclassified translation discrepancy"; product "pseudoautosomal GTP-binding protein-like protein"; protein_id "NP_036359.1"; db_xref "GeneID:8225"; db_xref "GI:6912588"; exon_number "1";
+NC_000024.9 RefSeq CDS 179433 179591 . - 1 gene_id "NC_000024.9:GTPBP6"; transcript_id "NM_012227.1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; exception "unclassified translation discrepancy"; product "pseudoautosomal GTP-binding protein-like protein"; protein_id "NP_036359.1"; db_xref "GeneID:8225"; db_xref "GI:6912588"; exon_number "2";
+NC_000024.9 RefSeq CDS 178086 178294 . - 1 gene_id "NC_000024.9:GTPBP6"; transcript_id "NM_012227.1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; exception "unclassified translation discrepancy"; product "pseudoautosomal GTP-binding protein-like protein"; protein_id "NP_036359.1"; db_xref "GeneID:8225"; db_xref "GI:6912588"; exon_number "3";
+NC_000024.9 RefSeq CDS 174399 174547 . - 2 gene_id "NC_000024.9:GTPBP6"; transcript_id "NM_012227.1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; exception "unclassified translation discrepancy"; product "pseudoautosomal GTP-binding protein-like protein"; protein_id "NP_036359.1"; db_xref "GeneID:8225"; db_xref "GI:6912588"; exon_number "4";
+NC_000024.9 RefSeq CDS 174027 174179 . - 0 gene_id "NC_000024.9:GTPBP6"; transcript_id "NM_012227.1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; exception "unclassified translation discrepancy"; product "pseudoautosomal GTP-binding protein-like protein"; protein_id "NP_036359.1"; db_xref "GeneID:8225"; db_xref "GI:6912588"; exon_number "5";
+NC_000024.9 RefSeq CDS 171741 171864 . - 0 gene_id "NC_000024.9:GTPBP6"; transcript_id "NM_012227.1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; exception "unclassified translation discrepancy"; product "pseudoautosomal GTP-binding protein-like protein"; protein_id "NP_036359.1"; db_xref "GeneID:8225"; db_xref "GI:6912588"; exon_number "6";
+NC_000024.9 RefSeq gene 231385 232067 . + . gene_id "NC_000024.9:NCRNA00107"; partial ""; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; db_xref "GeneID:283981"; db_xref "HGNC:27560";
+NC_000024.9 RefSeq exon 231385 232067 . + . gene_id "NC_000024.9:NCRNA00107"; transcript_id "NR_027232.1"; gbkey "misc_RNA"; product "non-protein coding RNA 107, transcript variant 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; db_xref "GeneID:283981"; exon_number "1";
+NC_000024.9 RefSeq exon 231385 232067 . + . gene_id "NC_000024.9:NCRNA00107"; transcript_id "NR_027231.1"; gbkey "misc_RNA"; product "non-protein coding RNA 107, transcript variant 2"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; db_xref "GeneID:283981"; exon_number "1";
+NC_000024.9 RefSeq gene 244970 297627 . - . gene_id "NC_000024.9:PPP2R3B"; partial ""; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; db_xref "GeneID:28227"; db_xref "HGNC:13417"; db_xref "MIM:300339";
+NC_000024.9 RefSeq exon 297103 297627 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_013239.3"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_013239.3"; db_xref "GeneID:28227"; db_xref "GI:41349492"; exon_number "1";
+NC_000024.9 RefSeq exon 272140 272325 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_013239.3"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_013239.3"; db_xref "GeneID:28227"; db_xref "GI:41349492"; exon_number "2";
+NC_000024.9 RefSeq exon 258325 258428 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_013239.3"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_013239.3"; db_xref "GeneID:28227"; db_xref "GI:41349492"; exon_number "3";
+NC_000024.9 RefSeq exon 257969 258071 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_013239.3"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_013239.3"; db_xref "GeneID:28227"; db_xref "GI:41349492"; exon_number "4";
+NC_000024.9 RefSeq exon 257436 257510 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_013239.3"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_013239.3"; db_xref "GeneID:28227"; db_xref "GI:41349492"; exon_number "5";
+NC_000024.9 RefSeq exon 256909 256995 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_013239.3"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_013239.3"; db_xref "GeneID:28227"; db_xref "GI:41349492"; exon_number "6";
+NC_000024.9 RefSeq exon 256251 256407 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_013239.3"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_013239.3"; db_xref "GeneID:28227"; db_xref "GI:41349492"; exon_number "7";
+NC_000024.9 RefSeq exon 252618 252666 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_013239.3"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_013239.3"; db_xref "GeneID:28227"; db_xref "GI:41349492"; exon_number "8";
+NC_000024.9 RefSeq exon 252042 252131 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_013239.3"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_013239.3"; db_xref "GeneID:28227"; db_xref "GI:41349492"; exon_number "9";
+NC_000024.9 RefSeq exon 251500 251675 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_013239.3"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_013239.3"; db_xref "GeneID:28227"; db_xref "GI:41349492"; exon_number "10";
+NC_000024.9 RefSeq exon 249513 249631 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_013239.3"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_013239.3"; db_xref "GeneID:28227"; db_xref "GI:41349492"; exon_number "11";
+NC_000024.9 RefSeq exon 249339 249445 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_013239.3"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_013239.3"; db_xref "GeneID:28227"; db_xref "GI:41349492"; exon_number "12";
+NC_000024.9 RefSeq exon 244970 245252 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_013239.3"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 1"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_013239.3"; db_xref "GeneID:28227"; db_xref "GI:41349492"; exon_number "13";
+NC_000024.9 RefSeq exon 252042 252590 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_199326.1"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 2"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_199326.1"; db_xref "GeneID:28227"; db_xref "GI:41349490"; exon_number "1";
+NC_000024.9 RefSeq exon 251500 251675 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_199326.1"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 2"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_199326.1"; db_xref "GeneID:28227"; db_xref "GI:41349490"; exon_number "2";
+NC_000024.9 RefSeq exon 249513 249631 . - . gene_id "NC_000024.9:PPP2R3B"; transcript_id "NM_199326.1"; gbkey "mRNA"; partial ""; product "protein phosphatase 2 (formerly 2A), regulatory subunit B\'\', beta, transcript variant 2"; note "Derived by automated computational analysis using gene prediction method: BestRefseq."; insd_transcript_id "NM_199326.1"; db_xref "GeneID:28227"; db_xref "GI:41349490"; exon_number "3";
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,30 @@
+#!/bin/bash
+set -e
+
+pkg=libgff-dev
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}"
+cp /usr/share/doc/python-pysam/tests/pysam_data/test.gtf -a "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+gunzip -r *
+
+echo 'Compiling ...'
+g++ TestGFFParse.cpp -lgff -Wall -o testlib
+echo '------------------------------'
+echo
+
+echo 'Test 1'
+./testlib test.gtf
+echo 'PASS'
+echo '-------------------------------'
+
+echo 'Test 2'
+./testlib example.gtf
+echo 'PASS'
+echo '-------------------------------'
=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,7 @@
+---
+Archive: GitHub
+Bug-Database: https://github.com/Kingsford-Group/libgff/issues
+Bug-Submit: https://github.com/Kingsford-Group/libgff/issues/new
+Changelog: https://github.com/Kingsford-Group/libgff/tags
+Repository: https://github.com/Kingsford-Group/libgff.git
+Repository-Browse: https://github.com/Kingsford-Group/libgff
View it on GitLab: https://salsa.debian.org/med-team/libgff/-/compare/3713ee29b376aeb3440a6c85e8dbc65b5a8ba47e...b9285521188196caa6e3e1b3e60b26e44085825b
--
View it on GitLab: https://salsa.debian.org/med-team/libgff/-/compare/3713ee29b376aeb3440a6c85e8dbc65b5a8ba47e...b9285521188196caa6e3e1b3e60b26e44085825b
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