[med-svn] [Git][med-team/trinculo][master] 2 commits: Provide a way to reconstruct text version of the binary data provided by...

Andreas Tille gitlab at salsa.debian.org
Thu Apr 9 20:49:13 BST 2020 


Andreas Tille pushed to branch master at Debian Med / trinculo


Commits:
3fefe8e6 by Andreas Tille at 2020-04-09T21:45:35+02:00
Provide a way to reconstruct text version of the binary data provided by upstream.  It can be converted back to byte-identical files

- - - - -
2a6cff05 by Andreas Tille at 2020-04-09T21:48:41+02:00
Add README.source

- - - - -


6 changed files:

- + debian/README.source
- + debian/missing-sources/genotypes.log
- + debian/missing-sources/genotypes.map
- + debian/missing-sources/genotypes.nosex
- + debian/missing-sources/genotypes.ped
- + debian/missing-sources/get_txt_examples


Changes:

=====================================
debian/README.source
=====================================
@@ -0,0 +1,9 @@
+Upstream provides a binary file examples/genotypes.bed without a text
+representation.  The script
+
+   debian/missing-sources/get_txt_examples
+
+provides a way to reconstruct text version of the binary data provided
+by upstream.  It can be converted back to byte-identical files.
+
+ -- Andreas Tille <tille at debian.org>  Thu, 09 Apr 2020 21:48:21 +0200


=====================================
debian/missing-sources/genotypes.log
=====================================
@@ -0,0 +1,47 @@
+
+ at ----------------------------------------------------------@
+|        PLINK!       |     v1.07      |   10/Aug/2009     |
+|----------------------------------------------------------|
+|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
+|----------------------------------------------------------|
+|  For documentation, citation & bug-report instructions:  |
+|        http://pngu.mgh.harvard.edu/purcell/plink/        |
+ at ----------------------------------------------------------@
+
+Skipping web check... [ --noweb ] 
+Writing this text to log file [ genotypes.log ]
+Analysis started: Thu Apr  9 21:45:13 2020
+
+Options in effect:
+	--bfile ../../examples/genotypes
+	--recode
+	--tab
+	--out genotypes
+	--noweb
+
+Reading map (extended format) from [ ../../examples/genotypes.bim ] 
+5 markers to be included from [ ../../examples/genotypes.bim ]
+Reading pedigree information from [ ../../examples/genotypes.fam ] 
+1000 individuals read from [ ../../examples/genotypes.fam ] 
+0 individuals with nonmissing phenotypes
+Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
+Missing phenotype value is also -9
+0 cases, 0 controls and 1000 missing
+0 males, 0 females, and 1000 of unspecified sex
+Warning, found 1000 individuals with ambiguous sex codes
+Writing list of these individuals to [ genotypes.nosex ]
+Reading genotype bitfile from [ ../../examples/genotypes.bed ] 
+Detected that binary PED file is v1.00 SNP-major mode
+Before frequency and genotyping pruning, there are 5 SNPs
+1000 founders and 0 non-founders found
+Total genotyping rate in remaining individuals is 1
+0 SNPs failed missingness test ( GENO > 1 )
+0 SNPs failed frequency test ( MAF < 0 )
+After frequency and genotyping pruning, there are 5 SNPs
+After filtering, 0 cases, 0 controls and 1000 missing
+After filtering, 0 males, 0 females, and 1000 of unspecified sex
+Writing recoded ped file to [ genotypes.ped ] 
+Writing new map file to [ genotypes.map ] 
+
+Analysis finished: Thu Apr  9 21:45:13 2020
+


=====================================
debian/missing-sources/genotypes.map
=====================================
@@ -0,0 +1,5 @@
+1	SNP1	0	1000
+1	SNP2	0	1200
+1	SNP3	0	1400
+2	SNP4	0	2000
+3	SNP5	0	1000


=====================================
debian/missing-sources/genotypes.nosex
=====================================
@@ -0,0 +1,1000 @@
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+IND899	IND899
+IND900	IND900
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+IND902	IND902
+IND903	IND903
+IND904	IND904
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+IND906	IND906
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+IND940	IND940
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+IND969	IND969
+IND970	IND970
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+IND975	IND975
+IND976	IND976
+IND977	IND977
+IND978	IND978
+IND979	IND979
+IND980	IND980
+IND981	IND981
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+IND983	IND983
+IND984	IND984
+IND985	IND985
+IND986	IND986
+IND987	IND987
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+IND989	IND989
+IND990	IND990
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+IND993	IND993
+IND994	IND994
+IND995	IND995
+IND996	IND996
+IND997	IND997
+IND998	IND998
+IND999	IND999
+IND1000	IND1000


=====================================
debian/missing-sources/genotypes.ped
=====================================
@@ -0,0 +1,1000 @@
+IND1	IND1	0	0	-9	-9	A A	A A	A A	A A	A C
+IND2	IND2	0	0	-9	-9	C A	C A	A A	A A	A A
+IND3	IND3	0	0	-9	-9	A A	C A	C A	C A	A A
+IND4	IND4	0	0	-9	-9	C C	C C	C C	A A	C C
+IND5	IND5	0	0	-9	-9	C C	C A	C A	A A	A C
+IND6	IND6	0	0	-9	-9	A A	A A	A A	C A	A C
+IND7	IND7	0	0	-9	-9	A A	A A	A A	C A	A C
+IND8	IND8	0	0	-9	-9	A A	A A	C A	C A	C C
+IND9	IND9	0	0	-9	-9	C A	C A	A A	A A	A C
+IND10	IND10	0	0	-9	-9	A A	A A	A A	C A	A C
+IND11	IND11	0	0	-9	-9	A A	A A	A A	C A	A A
+IND12	IND12	0	0	-9	-9	C C	C A	C A	A A	C C
+IND13	IND13	0	0	-9	-9	C A	A A	A A	A A	C C
+IND14	IND14	0	0	-9	-9	C C	C A	C A	A A	A A
+IND15	IND15	0	0	-9	-9	A A	A A	C A	A A	C C
+IND16	IND16	0	0	-9	-9	A A	A A	A A	A A	A C
+IND17	IND17	0	0	-9	-9	A A	A A	A A	C A	C C
+IND18	IND18	0	0	-9	-9	A A	C A	C C	C A	C C
+IND19	IND19	0	0	-9	-9	A A	A A	A A	C A	C C
+IND20	IND20	0	0	-9	-9	C A	A A	A A	A A	A A
+IND21	IND21	0	0	-9	-9	A A	A A	A A	C A	A A
+IND22	IND22	0	0	-9	-9	A A	A A	A A	A A	C C
+IND23	IND23	0	0	-9	-9	A A	A A	C A	C C	A A
+IND24	IND24	0	0	-9	-9	C A	A A	C A	C A	A C
+IND25	IND25	0	0	-9	-9	A A	A A	A A	A A	A C
+IND26	IND26	0	0	-9	-9	C A	C A	C A	A A	A A
+IND27	IND27	0	0	-9	-9	A A	A A	A A	C A	C C
+IND28	IND28	0	0	-9	-9	A A	A A	C A	A A	A C
+IND29	IND29	0	0	-9	-9	A A	A A	A A	C A	A C
+IND30	IND30	0	0	-9	-9	C A	C A	A A	C C	A C
+IND31	IND31	0	0	-9	-9	C A	A A	A A	C A	A C
+IND32	IND32	0	0	-9	-9	A A	A A	A A	A A	C C
+IND33	IND33	0	0	-9	-9	A A	A A	A A	A A	A C
+IND34	IND34	0	0	-9	-9	A A	A A	A A	C A	A A
+IND35	IND35	0	0	-9	-9	C A	C A	C A	A A	A A
+IND36	IND36	0	0	-9	-9	A A	A A	A A	C C	A C
+IND37	IND37	0	0	-9	-9	C A	A A	A A	C A	C C
+IND38	IND38	0	0	-9	-9	C C	C C	C C	A A	C C
+IND39	IND39	0	0	-9	-9	A A	A A	A A	A A	C C
+IND40	IND40	0	0	-9	-9	A A	A A	A A	A A	C C
+IND41	IND41	0	0	-9	-9	C A	A A	A A	A A	A C
+IND42	IND42	0	0	-9	-9	C A	C A	A A	C A	A C
+IND43	IND43	0	0	-9	-9	A A	A A	A A	C A	C C
+IND44	IND44	0	0	-9	-9	A A	A A	A A	A A	A C
+IND45	IND45	0	0	-9	-9	C A	C A	A A	A A	C C
+IND46	IND46	0	0	-9	-9	A A	A A	A A	A A	C C
+IND47	IND47	0	0	-9	-9	C A	C C	C C	C C	A C
+IND48	IND48	0	0	-9	-9	A A	A A	A A	A A	C C
+IND49	IND49	0	0	-9	-9	A A	A A	A A	A A	C C
+IND50	IND50	0	0	-9	-9	C A	C A	C A	A A	C C
+IND51	IND51	0	0	-9	-9	C A	A A	A A	A A	A C
+IND52	IND52	0	0	-9	-9	A A	A A	A A	C A	A C
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+IND54	IND54	0	0	-9	-9	C A	C A	C C	A A	C C
+IND55	IND55	0	0	-9	-9	A A	A A	C A	C A	A A
+IND56	IND56	0	0	-9	-9	A A	A A	A A	C C	A C
+IND57	IND57	0	0	-9	-9	C A	C A	C A	C A	A C
+IND58	IND58	0	0	-9	-9	A A	C A	C A	A A	C C
+IND59	IND59	0	0	-9	-9	C A	C C	C A	C A	A C
+IND60	IND60	0	0	-9	-9	A A	A A	A A	A A	A C
+IND61	IND61	0	0	-9	-9	A A	A A	C A	A A	C C
+IND62	IND62	0	0	-9	-9	A A	A A	C A	C C	A C
+IND63	IND63	0	0	-9	-9	C C	C A	A A	A A	A A
+IND64	IND64	0	0	-9	-9	C C	C C	C C	C A	C C
+IND65	IND65	0	0	-9	-9	C C	C A	A A	C C	C C
+IND66	IND66	0	0	-9	-9	A A	A A	C A	A A	A C
+IND67	IND67	0	0	-9	-9	A A	A A	A A	A A	A C
+IND68	IND68	0	0	-9	-9	A A	A A	A A	C A	C C
+IND69	IND69	0	0	-9	-9	C A	C A	C A	C A	C C
+IND70	IND70	0	0	-9	-9	C A	C A	C A	C A	C C
+IND71	IND71	0	0	-9	-9	C A	C A	A A	A A	A C
+IND72	IND72	0	0	-9	-9	C A	A A	A A	C A	C C
+IND73	IND73	0	0	-9	-9	C A	C A	C A	A A	A C
+IND74	IND74	0	0	-9	-9	A A	C A	C A	A A	A C
+IND75	IND75	0	0	-9	-9	A A	C A	C A	C A	C C
+IND76	IND76	0	0	-9	-9	C A	C A	A A	C C	A A
+IND77	IND77	0	0	-9	-9	A A	A A	A A	A A	A C
+IND78	IND78	0	0	-9	-9	C A	C A	C A	A A	A C
+IND79	IND79	0	0	-9	-9	C A	A A	A A	A A	C C
+IND80	IND80	0	0	-9	-9	C A	A A	A A	C A	A C
+IND81	IND81	0	0	-9	-9	A A	A A	A A	A A	C C
+IND82	IND82	0	0	-9	-9	C A	C A	C A	A A	C C
+IND83	IND83	0	0	-9	-9	C A	C A	C A	A A	A A
+IND84	IND84	0	0	-9	-9	A A	A A	A A	A A	C C
+IND85	IND85	0	0	-9	-9	A A	A A	A A	A A	C C
+IND86	IND86	0	0	-9	-9	C A	C A	A A	C A	C C
+IND87	IND87	0	0	-9	-9	C A	C A	C A	A A	A C
+IND88	IND88	0	0	-9	-9	C A	A A	A A	A A	C C
+IND89	IND89	0	0	-9	-9	A A	A A	A A	C A	A A
+IND90	IND90	0	0	-9	-9	A A	A A	C A	C A	A A
+IND91	IND91	0	0	-9	-9	C A	C A	C A	A A	A C
+IND92	IND92	0	0	-9	-9	A A	C A	A A	A A	C C
+IND93	IND93	0	0	-9	-9	A A	A A	A A	C A	A C
+IND94	IND94	0	0	-9	-9	C A	C A	C A	C A	A C
+IND95	IND95	0	0	-9	-9	A A	A A	A A	A A	C C
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+IND99	IND99	0	0	-9	-9	C A	A A	A A	A A	C C
+IND100	IND100	0	0	-9	-9	A A	A A	C A	C A	C C
+IND101	IND101	0	0	-9	-9	C A	A A	A A	A A	C C
+IND102	IND102	0	0	-9	-9	A A	A A	A A	A A	A C
+IND103	IND103	0	0	-9	-9	C A	C A	A A	C A	A A
+IND104	IND104	0	0	-9	-9	C C	C A	C A	A A	A A
+IND105	IND105	0	0	-9	-9	C A	C A	C A	C C	A C
+IND106	IND106	0	0	-9	-9	A A	A A	A A	C A	C C
+IND107	IND107	0	0	-9	-9	C A	A A	A A	A A	C C
+IND108	IND108	0	0	-9	-9	C A	C A	A A	A A	A C
+IND109	IND109	0	0	-9	-9	A A	A A	C A	A A	A C
+IND110	IND110	0	0	-9	-9	C A	C A	C A	C A	A C
+IND111	IND111	0	0	-9	-9	A A	A A	A A	C A	A C
+IND112	IND112	0	0	-9	-9	C C	C C	C C	C A	A C
+IND113	IND113	0	0	-9	-9	C A	A A	A A	A A	A C
+IND114	IND114	0	0	-9	-9	A A	A A	C A	A A	A C
+IND115	IND115	0	0	-9	-9	C C	C A	C A	C A	A C
+IND116	IND116	0	0	-9	-9	C A	A A	A A	C A	C C
+IND117	IND117	0	0	-9	-9	C A	C A	C C	A A	A C
+IND118	IND118	0	0	-9	-9	C A	C A	C A	C A	A C
+IND119	IND119	0	0	-9	-9	A A	A A	A A	A A	C C
+IND120	IND120	0	0	-9	-9	A A	A A	A A	C C	C C
+IND121	IND121	0	0	-9	-9	C C	C C	C A	A A	A A
+IND122	IND122	0	0	-9	-9	C A	C A	A A	C A	C C
+IND123	IND123	0	0	-9	-9	A A	C A	C A	A A	A C
+IND124	IND124	0	0	-9	-9	A A	A A	A A	A A	A C
+IND125	IND125	0	0	-9	-9	C A	A A	A A	C A	C C
+IND126	IND126	0	0	-9	-9	C A	A A	A A	C A	A C
+IND127	IND127	0	0	-9	-9	C A	C A	C C	A A	C C
+IND128	IND128	0	0	-9	-9	C A	C A	C A	C A	C C
+IND129	IND129	0	0	-9	-9	A A	A A	A A	A A	C C
+IND130	IND130	0	0	-9	-9	C A	A A	A A	C C	A C
+IND131	IND131	0	0	-9	-9	C A	C A	A A	A A	A C
+IND132	IND132	0	0	-9	-9	C A	A A	C A	A A	A C
+IND133	IND133	0	0	-9	-9	C C	C C	C A	A A	A C
+IND134	IND134	0	0	-9	-9	A A	A A	A A	C A	C C
+IND135	IND135	0	0	-9	-9	C C	C C	C C	A A	A C
+IND136	IND136	0	0	-9	-9	C A	A A	A A	C A	C C
+IND137	IND137	0	0	-9	-9	C A	C A	C A	C A	A C
+IND138	IND138	0	0	-9	-9	C A	C A	C A	A A	C C
+IND139	IND139	0	0	-9	-9	C A	C A	C A	C A	C C
+IND140	IND140	0	0	-9	-9	A A	A A	A A	A A	C C
+IND141	IND141	0	0	-9	-9	C A	C A	C A	A A	A C
+IND142	IND142	0	0	-9	-9	C A	A A	A A	A A	C C
+IND143	IND143	0	0	-9	-9	A A	A A	A A	C A	A C
+IND144	IND144	0	0	-9	-9	A A	C A	C A	C A	A C
+IND145	IND145	0	0	-9	-9	C A	C A	A A	C A	A C
+IND146	IND146	0	0	-9	-9	A A	C A	C A	C A	C C
+IND147	IND147	0	0	-9	-9	C A	C A	C A	A A	A C
+IND148	IND148	0	0	-9	-9	C A	A A	A A	A A	C C
+IND149	IND149	0	0	-9	-9	C A	A A	A A	C A	C C
+IND150	IND150	0	0	-9	-9	C A	C A	A A	C A	C C
+IND151	IND151	0	0	-9	-9	A A	C A	A A	C A	C C
+IND152	IND152	0	0	-9	-9	C A	C C	C C	C A	C C
+IND153	IND153	0	0	-9	-9	A A	A A	A A	C A	A C
+IND154	IND154	0	0	-9	-9	C A	C A	C A	A A	A C
+IND155	IND155	0	0	-9	-9	A A	A A	A A	C A	A C
+IND156	IND156	0	0	-9	-9	C A	A A	A A	C A	A C
+IND157	IND157	0	0	-9	-9	A A	A A	A A	A A	C C
+IND158	IND158	0	0	-9	-9	C A	C A	C A	C A	C C
+IND159	IND159	0	0	-9	-9	C A	A A	A A	C A	C C
+IND160	IND160	0	0	-9	-9	A A	A A	A A	C A	C C
+IND161	IND161	0	0	-9	-9	A A	A A	A A	A A	A A
+IND162	IND162	0	0	-9	-9	A A	A A	A A	A A	C C
+IND163	IND163	0	0	-9	-9	C A	C A	C A	A A	C C
+IND164	IND164	0	0	-9	-9	C A	C A	C A	C A	C C
+IND165	IND165	0	0	-9	-9	C A	C A	A A	A A	A C
+IND166	IND166	0	0	-9	-9	A A	A A	C A	A A	C C
+IND167	IND167	0	0	-9	-9	A A	A A	A A	C A	C C
+IND168	IND168	0	0	-9	-9	A A	A A	A A	C C	C C
+IND169	IND169	0	0	-9	-9	C A	C A	A A	C A	C C
+IND170	IND170	0	0	-9	-9	A A	A A	C A	C A	A C
+IND171	IND171	0	0	-9	-9	C C	C C	C C	A A	C C
+IND172	IND172	0	0	-9	-9	C A	C A	C A	A A	C C
+IND173	IND173	0	0	-9	-9	A A	A A	A A	A A	C C
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+IND175	IND175	0	0	-9	-9	A A	C A	C A	C C	A C
+IND176	IND176	0	0	-9	-9	A A	A A	A A	C A	A C
+IND177	IND177	0	0	-9	-9	A A	C A	A A	C A	C C
+IND178	IND178	0	0	-9	-9	A A	C A	A A	A A	A C
+IND179	IND179	0	0	-9	-9	A A	A A	A A	C A	C C
+IND180	IND180	0	0	-9	-9	C C	C A	A A	A A	A C
+IND181	IND181	0	0	-9	-9	C A	C A	A A	A A	A C
+IND182	IND182	0	0	-9	-9	C A	C A	C A	C A	A C
+IND183	IND183	0	0	-9	-9	C A	A A	A A	C A	C C
+IND184	IND184	0	0	-9	-9	C A	C A	A A	C A	A C
+IND185	IND185	0	0	-9	-9	A A	A A	A A	A A	C C
+IND186	IND186	0	0	-9	-9	A A	A A	A A	C C	A C
+IND187	IND187	0	0	-9	-9	A A	A A	A A	A A	C C
+IND188	IND188	0	0	-9	-9	A A	A A	C A	C A	A C
+IND189	IND189	0	0	-9	-9	A A	A A	A A	A A	C C
+IND190	IND190	0	0	-9	-9	C A	A A	A A	C C	A A
+IND191	IND191	0	0	-9	-9	C A	A A	A A	C A	A C
+IND192	IND192	0	0	-9	-9	C A	C C	C C	C C	C C
+IND193	IND193	0	0	-9	-9	A A	A A	A A	A A	C C
+IND194	IND194	0	0	-9	-9	A A	A A	A A	A A	A C
+IND195	IND195	0	0	-9	-9	C C	C A	C A	A A	A A
+IND196	IND196	0	0	-9	-9	A A	A A	C A	C C	A C
+IND197	IND197	0	0	-9	-9	C A	A A	A A	A A	A C
+IND198	IND198	0	0	-9	-9	A A	A A	A A	C A	C C
+IND199	IND199	0	0	-9	-9	A A	A A	A A	C A	C C
+IND200	IND200	0	0	-9	-9	A A	A A	A A	C A	A C
+IND201	IND201	0	0	-9	-9	A A	A A	A A	A A	C C
+IND202	IND202	0	0	-9	-9	C A	C A	C A	C A	A A
+IND203	IND203	0	0	-9	-9	C C	C C	C A	A A	C C
+IND204	IND204	0	0	-9	-9	C C	C C	C C	C A	C C
+IND205	IND205	0	0	-9	-9	A A	C A	A A	A A	A A
+IND206	IND206	0	0	-9	-9	A A	A A	A A	C C	A C
+IND207	IND207	0	0	-9	-9	C A	C A	A A	A A	C C
+IND208	IND208	0	0	-9	-9	C A	C A	A A	A A	A C
+IND209	IND209	0	0	-9	-9	C A	A A	A A	A A	C C
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+IND940	IND940	0	0	-9	-9	C A	A A	A A	A A	A C
+IND941	IND941	0	0	-9	-9	A A	A A	C A	C A	C C
+IND942	IND942	0	0	-9	-9	C C	C A	C A	A A	C C
+IND943	IND943	0	0	-9	-9	A A	A A	A A	A A	C C
+IND944	IND944	0	0	-9	-9	A A	A A	A A	C A	A A
+IND945	IND945	0	0	-9	-9	A A	A A	A A	A A	C C
+IND946	IND946	0	0	-9	-9	A A	A A	A A	A A	C C
+IND947	IND947	0	0	-9	-9	C A	A A	A A	C A	A A
+IND948	IND948	0	0	-9	-9	C A	A A	A A	A A	C C
+IND949	IND949	0	0	-9	-9	C A	A A	A A	A A	C C
+IND950	IND950	0	0	-9	-9	C A	C A	C A	A A	C C
+IND951	IND951	0	0	-9	-9	A A	C A	C A	A A	C C
+IND952	IND952	0	0	-9	-9	A A	A A	A A	C A	A C
+IND953	IND953	0	0	-9	-9	A A	C A	A A	A A	A C
+IND954	IND954	0	0	-9	-9	A A	A A	A A	A A	C C
+IND955	IND955	0	0	-9	-9	C A	A A	A A	A A	C C
+IND956	IND956	0	0	-9	-9	A A	A A	A A	A A	A A
+IND957	IND957	0	0	-9	-9	C A	A A	A A	A A	A C
+IND958	IND958	0	0	-9	-9	C A	A A	C A	A A	C C
+IND959	IND959	0	0	-9	-9	A A	A A	A A	A A	C C
+IND960	IND960	0	0	-9	-9	A A	A A	A A	A A	C C
+IND961	IND961	0	0	-9	-9	C A	A A	A A	C A	A A
+IND962	IND962	0	0	-9	-9	C A	C A	C A	C A	C C
+IND963	IND963	0	0	-9	-9	C A	A A	A A	A A	A C
+IND964	IND964	0	0	-9	-9	C A	A A	A A	C A	A C
+IND965	IND965	0	0	-9	-9	C A	A A	A A	A A	C C
+IND966	IND966	0	0	-9	-9	A A	A A	C A	A A	C C
+IND967	IND967	0	0	-9	-9	A A	C A	A A	A A	C C
+IND968	IND968	0	0	-9	-9	C A	A A	A A	C A	C C
+IND969	IND969	0	0	-9	-9	A A	A A	A A	A A	A C
+IND970	IND970	0	0	-9	-9	C C	C C	C A	A A	C C
+IND971	IND971	0	0	-9	-9	C A	A A	A A	C A	A C
+IND972	IND972	0	0	-9	-9	C A	C A	C A	C A	A C
+IND973	IND973	0	0	-9	-9	A A	A A	A A	C C	C C
+IND974	IND974	0	0	-9	-9	C A	A A	A A	C A	A C
+IND975	IND975	0	0	-9	-9	A A	A A	A A	A A	A A
+IND976	IND976	0	0	-9	-9	A A	A A	A A	A A	A C
+IND977	IND977	0	0	-9	-9	A A	C A	C A	C A	A C
+IND978	IND978	0	0	-9	-9	C A	A A	C A	C C	A C
+IND979	IND979	0	0	-9	-9	A A	A A	A A	A A	C C
+IND980	IND980	0	0	-9	-9	C A	C A	C A	A A	A A
+IND981	IND981	0	0	-9	-9	A A	A A	A A	C A	A C
+IND982	IND982	0	0	-9	-9	A A	C A	C C	A A	A A
+IND983	IND983	0	0	-9	-9	C A	C A	C A	C A	A A
+IND984	IND984	0	0	-9	-9	A A	A A	A A	C C	C C
+IND985	IND985	0	0	-9	-9	A A	A A	A A	A A	C C
+IND986	IND986	0	0	-9	-9	A A	A A	A A	A A	C C
+IND987	IND987	0	0	-9	-9	A A	A A	A A	A A	C C
+IND988	IND988	0	0	-9	-9	C A	C A	A A	C A	C C
+IND989	IND989	0	0	-9	-9	C A	A A	A A	C A	C C
+IND990	IND990	0	0	-9	-9	A A	A A	A A	C A	A C
+IND991	IND991	0	0	-9	-9	C A	C A	C C	A A	A C
+IND992	IND992	0	0	-9	-9	C A	A A	A A	A A	A C
+IND993	IND993	0	0	-9	-9	C A	C A	C A	A A	C C
+IND994	IND994	0	0	-9	-9	C A	C A	C A	C A	A C
+IND995	IND995	0	0	-9	-9	C C	C C	C C	A A	C C
+IND996	IND996	0	0	-9	-9	A A	A A	A A	A A	C C
+IND997	IND997	0	0	-9	-9	A A	A A	C A	A A	A A
+IND998	IND998	0	0	-9	-9	A A	A A	C A	A A	C C
+IND999	IND999	0	0	-9	-9	C A	C A	C A	A A	A C
+IND1000	IND1000	0	0	-9	-9	A A	A A	A A	A A	A C


=====================================
debian/missing-sources/get_txt_examples
=====================================
@@ -0,0 +1,13 @@
+#!/bin/sh
+
+if ! which plink1 >/dev/null ; then
+    echo "You need to"
+    echo "   sudo apt-get install plink"
+    exit
+fi
+
+plink1 --bfile ../../examples/genotypes --recode --tab --out genotypes --noweb
+
+mkdir -p examples_orig
+cd examples_orig
+plink1 --file ../genotypes --make-bed --out genotypes --noweb



View it on GitLab: https://salsa.debian.org/med-team/trinculo/-/compare/0aa2665bd9eced8b48827bcdc3a01934b431f34e...2a6cff05aa20d910c078dab9b8a2aa93c1f1dbd4

-- 
View it on GitLab: https://salsa.debian.org/med-team/trinculo/-/compare/0aa2665bd9eced8b48827bcdc3a01934b431f34e...2a6cff05aa20d910c078dab9b8a2aa93c1f1dbd4
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