[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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