details:
http://www.bx.psu.edu/hg/galaxy/rev/28ec4708840f
changeset: 2933:28ec4708840f
user: Ross Lazarus <ross.lazarus(a)gmail.com>
date: Thu Oct 29 17:57:30 2009 -0400
description:
updated rgenetics test files
diffstat:
test-data/tinywga.bed | 2 +-
test-data/tinywga.bim | 35 ++++++++---
test-data/tinywga.fam | 130 +++++++++++++------------------------------
test-data/tinywga.map | 35 ++++++++---
test-data/tinywga.ped | 130 +++++++++++++------------------------------
test-data/tinywga.pphe | 42 ++++++++++++++
6 files changed, 173 insertions(+), 201 deletions(-)
diffs (400 lines):
diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.bed
--- a/test-data/tinywga.bed Thu Oct 29 13:34:44 2009 -0400
+++ b/test-data/tinywga.bed Thu Oct 29 17:57:30 2009 -0400
@@ -1,1 +1,1 @@
-lÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿï¾î¸ÿÿüþ¿ÿ¿ûú¿¿ï/ÿÿþÿï¯ê¸ëê°®¾î®ãê¸;ì/âïú¯ï¯Îê¼ïâ°¯þÏªã¯ø+ì?âÿú¯ïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿïÿÿÿÿÿºÿÿþ¯þï¿ÿ»ÿÿþÿÿÿïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿÿÿÿÿþïÿÿÿþÿÿÿÿûÿûÿÿÿ»ÿïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿïëÿê¾ÿºúïþ¯îë¿þ;¯>âïþ»
\ No newline at end of file
+lÿëþ¿¾+êóª¿ü £ïªîþ¨êÿïªûÿÿÿÿÿÿþﮨª"ëú £ïªîþ¨ÿÿ»ÿÿïïþÿèÿþ"ÿ«ïªîþ¨:*ÿïêüº.«ë:*ÿïêüº.«ëÿÿÿÿ¯ÿ¿ïþ¿ÿþªÿ¯û¿ïþ¿:*»ïêìª,«À:*»ïêìª,«Àÿëþ¿¾+êóª¿ÿÿÿÿûÿúÿÿÿÿÿÿÿÿÿ¿þ¿ÿëþ¿¾+ê󪿺ûÿÿ¿»ÿÿþ¿êÿÿªûÿÿÿÿÿºûÿÿ¿»ÿÿþ¿mÿÿÿýÿÿÿÿÿ
ú¢ª±«¯ü(:ú¢ÿ¿«¯ü(:ú¢ÿ¿«¯ü(:ú¢ÿ¿«¯ü(
\ No newline at end of file
diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.bim
--- a/test-data/tinywga.bim Thu Oct 29 13:34:44 2009 -0400
+++ b/test-data/tinywga.bim Thu Oct 29 17:57:30 2009 -0400
@@ -1,10 +1,25 @@
-22 rs5992809 16.5965 16596539 0 C
-22 rs12168131 16.6573 16657262 G A
-22 rs390041 16.6629 16662916 T C
-22 rs437633 16.6697 16669684 A G
-22 rs450960 16.6909 16690858 T C
-22 rs450975 16.6909 16690887 T C
-22 rs451740 16.6912 16691174 T C
-22 rs8139723 16.6917 16691696 T C
-22 rs405490 16.6922 16692175 G A
-22 rs415170 16.6935 16693517 G C
+22 rs2283802 0 21784722 4 2
+22 rs2267000 0 21785366 4 2
+22 rs16997606 0 21794754 1 3
+22 rs4820537 0 21794810 1 3
+22 rs3788347 0 21797804 3 1
+22 rs756632 0 21799918 4 2
+22 rs4820539 0 21807970 1 3
+22 rs2283804 0 21820335 1 2
+22 rs2267006 0 21820990 3 1
+22 rs4822363 0 21821000 4 2
+22 rs5751592 0 21827674 4 2
+22 rs5759608 0 21832708 2 4
+22 rs5759612 0 21833170 3 1
+22 rs2267009 0 21860168 3 4
+22 rs2267010 0 21864366 3 1
+22 rs5759636 0 21868698 4 2
+22 rs2071436 0 21871488 4 2
+22 rs2267013 0 21875879 3 1
+22 rs6003566 0 21889806 3 1
+22 rs2256725 0 21892891 2 1
+22 rs12160770 0 21892925 1 3
+22 rs5751611 0 21896019 2 4
+22 rs762601 0 21898858 1 3
+22 rs2156921 0 21899063 3 1
+22 rs4822375 0 21905642 1 3
diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.fam
--- a/test-data/tinywga.fam Thu Oct 29 13:34:44 2009 -0400
+++ b/test-data/tinywga.fam Thu Oct 29 17:57:30 2009 -0400
@@ -1,90 +1,40 @@
-CH18526 NA18526 0 0 2 1
-CH18524 NA18524 0 0 1 1
-CH18529 NA18529 0 0 2 1
-CH18558 NA18558 0 0 1 1
-CH18532 NA18532 0 0 2 1
-CH18561 NA18561 0 0 1 1
-CH18562 NA18562 0 0 1 1
-CH18537 NA18537 0 0 2 2
-CH18603 NA18603 0 0 1 2
-CH18540 NA18540 0 0 2 1
-CH18605 NA18605 0 0 1 1
-CH18542 NA18542 0 0 2 1
-CH18545 NA18545 0 0 2 1
-CH18572 NA18572 0 0 1 2
-CH18547 NA18547 0 0 2 2
-CH18609 NA18609 0 0 1 1
-CH18550 NA18550 0 0 2 1
-CH18608 NA18608 0 0 1 1
-CH18552 NA18552 0 0 2 1
-CH18611 NA18611 0 0 1 1
-CH18555 NA18555 0 0 2 1
-CH18564 NA18564 0 0 2 2
-CH18566 NA18566 0 0 2 1
-CH18563 NA18563 0 0 1 1
-CH18570 NA18570 0 0 2 1
-CH18612 NA18612 0 0 1 2
-CH18571 NA18571 0 0 2 1
-CH18620 NA18620 0 0 1 1
-CH18621 NA18621 0 0 1 1
-CH18594 NA18594 0 0 2 1
-CH18622 NA18622 0 0 1 2
-CH18573 NA18573 0 0 2 2
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-CH18576 NA18576 0 0 2 1
-CH18577 NA18577 0 0 2 1
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-CH18579 NA18579 0 0 2 1
-CH18632 NA18632 0 0 1 2
-CH18582 NA18582 0 0 2 1
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-CH18635 NA18635 0 0 1 2
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-CH18593 NA18593 0 0 2 2
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-JA18942 NA18942 0 0 2 2
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-JA18943 NA18943 0 0 1 2
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-JA18949 NA18949 0 0 2 2
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-JA18956 NA18956 0 0 2 2
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-JA18953 NA18953 0 0 1 1
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-JA18960 NA18960 0 0 1 2
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-JA18965 NA18965 0 0 1 2
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-JA18990 NA18990 0 0 1 1
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-JA18998 NA18998 0 0 2 2
-JA19000 NA19000 0 0 1 2
-JA19005 NA19005 0 0 1 2
-JA18999 NA18999 0 0 2 2
-JA19007 NA19007 0 0 1 2
-JA19003 NA19003 0 0 2 2
-JA19012 NA19012 0 0 1 2
+101 1 3 2 2 2
+101 2 0 0 2 1
+101 3 0 0 1 1
+105 1 3 2 2 2
+105 2 0 0 2 1
+105 3 0 0 1 1
+112 1 3 2 1 2
+112 2 0 0 2 1
+112 3 0 0 1 1
+117 1 3 2 2 2
+117 2 0 0 2 1
+117 3 0 0 1 1
+12 1 3 2 1 2
+12 2 0 0 2 1
+12 3 0 0 1 1
+13 1 3 2 1 2
+13 2 0 0 2 1
+13 3 0 0 1 1
+1334 1 10 11 1 2
+1334 10 0 0 1 1
+1334 11 0 0 2 1
+1334 12 0 0 1 1
+1334 13 0 0 2 1
+1334 2 12 13 2 2
+1340 1 9 10 1 2
+1340 10 0 0 2 1
+1340 11 0 0 1 1
+1340 12 0 0 2 1
+1340 2 11 12 2 2
+1340 9 0 0 1 1
+1341 1 11 12 1 1
+1341 11 0 0 1 1
+1341 12 0 0 2 1
+1341 13 0 0 1 1
+1341 14 0 0 2 1
+1341 2 13 14 2 1
+1344 1 12 13 1 1
+1344 12 0 0 1 1
+1344 13 0 0 2 1
+1345 12 0 0 1 1
diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.map
--- a/test-data/tinywga.map Thu Oct 29 13:34:44 2009 -0400
+++ b/test-data/tinywga.map Thu Oct 29 17:57:30 2009 -0400
@@ -1,10 +1,25 @@
-22 rs5992809 16.5965 16596539
-22 rs12168131 16.6573 16657262
-22 rs390041 16.6629 16662916
-22 rs437633 16.6697 16669684
-22 rs450960 16.6909 16690858
-22 rs450975 16.6909 16690887
-22 rs451740 16.6912 16691174
-22 rs8139723 16.6917 16691696
-22 rs405490 16.6922 16692175
-22 rs415170 16.6935 16693517
+22 rs2283802 0 21784722
+22 rs2267000 0 21785366
+22 rs16997606 0 21794754
+22 rs4820537 0 21794810
+22 rs3788347 0 21797804
+22 rs756632 0 21799918
+22 rs4820539 0 21807970
+22 rs2283804 0 21820335
+22 rs2267006 0 21820990
+22 rs4822363 0 21821000
+22 rs5751592 0 21827674
+22 rs5759608 0 21832708
+22 rs5759612 0 21833170
+22 rs2267009 0 21860168
+22 rs2267010 0 21864366
+22 rs5759636 0 21868698
+22 rs2071436 0 21871488
+22 rs2267013 0 21875879
+22 rs6003566 0 21889806
+22 rs2256725 0 21892891
+22 rs12160770 0 21892925
+22 rs5751611 0 21896019
+22 rs762601 0 21898858
+22 rs2156921 0 21899063
+22 rs4822375 0 21905642
diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.ped
--- a/test-data/tinywga.ped Thu Oct 29 13:34:44 2009 -0400
+++ b/test-data/tinywga.ped Thu Oct 29 17:57:30 2009 -0400
@@ -1,90 +1,40 @@
-CH18526 NA18526 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
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-CH18558 NA18558 0 0 1 1 C C A A C C G G C C C C C C C C A A C C
-CH18532 NA18532 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
-CH18561 NA18561 0 0 1 1 C C A A C C G G T C C C T C C C G A G C
-CH18562 NA18562 0 0 1 1 C C G A T C A G T C C C T C C C G A G C
-CH18537 NA18537 0 0 2 2 C C A A T C A G C C C C C C C C A A C C
-CH18603 NA18603 0 0 1 2 C C G A T C A G C C C C C C C C A A C C
-CH18540 NA18540 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
-CH18605 NA18605 0 0 1 1 C C A A T T A A C C C C C C C C A A C C
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-CH18572 NA18572 0 0 1 2 C C A A T C A G C C C C C C C C A A G C
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-CH18609 NA18609 0 0 1 1 C C A A C C G G C C C C C C C C A A C C
-CH18550 NA18550 0 0 2 1 C C G G T T A A T C C C T C T C G A G C
-CH18608 NA18608 0 0 1 1 C C G A T C G G C C C C C C C C A A C C
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-CH18636 NA18636 0 0 1 1 C C A A T C A A T C T C T C C C G A G C
-CH18593 NA18593 0 0 2 2 C C A A C C G G T C T C T C C C G A G C
-CH18637 NA18637 0 0 1 1 C C A A T C A G T C T C T C C C G A G C
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-JA18987 NA18987 0 0 2 2 C C A A C C G G C C C C C C C C A A C C
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-JA18994 NA18994 0 0 1 2 C C G A T C A G C C C C C C C C A A G C
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2 1 0 0 2 2 1 3 3 1 1 3
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2 1 3 3 2 2 1 3 3 1 1 3
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1 1 1 3 2 4 3 3 1 1 3 3
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2 1 0 0 2 2 1 1 3 3 1 1
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1 1 3 3 2 4 1 3 3 1 1 3
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2 1 3 3 2 4 1 3 3 1 1 3
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1 1 3 3 4 4 3 3 1 1 3 3
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1 1 3 3 4 4 3 3 1 1 3 3
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1 1 3 3 2 4 1 3 3 1 1 3
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1 1 3 3 2 2 1 1 3 3 1 1
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1 1 3 3 2 4 1 3 3 1 1 3
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1 1 3 3 2 4 1 3 3 1 1 3
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1 1 3 3 2 4 3 3 1 1 3 3
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1 1 3 3 2 4 3 3 1 1 3 3
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1 1 3 3 2 4 3 3 1 1 3 3
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1 1 3 3 2 4 3 3 1 1 3 3
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1 1 0 0 0 0 3 3 1 1 3 3
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1 1 3 3 2 2 3 3 1 1 3 3
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1 1 1 1 3 3 4 4 3 3 1 1 3 3
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1 2 1 3 3 2 4 1 3 3 1 1 3
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diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.pphe
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tinywga.pphe Thu Oct 29 17:57:30 2009 -0400
@@ -0,0 +1,42 @@
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+