details: http://www.bx.psu.edu/hg/galaxy/rev/28ec4708840f changeset: 2933:28ec4708840f user: Ross Lazarus <ross.lazarus(a)gmail.com&gt; 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 @@ -l
ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿï¾î¸ÿÿüþ¿ÿ¿ûú¿¿ï/ÿÿþÿ﯎ê¸ëê°®¾î®ãê¸;ì/âïú¯ï¯Îê¼ïâ°¯þϪã¯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 +l
ÿëþ¿¾+ê󪿊üŠ £ïªîþ¨êÿïªûÿÿÿÿÿÿþﮨª"ë€ú £ïªîþ¨ÿÿ»ÿÿïïþÿèÿþ"ÿ«ïªîþ¨:*ÿïêüº.«ë:*ÿïêüº.«ëÿÿÿÿ¯ÿ¿ïþ¿ÿþªÿ¯û¿ïþ¿:*»ïêìª,«À:*»ïêìª,«Àÿëþ¿¾+êóª¿ÿÿÿÿûÿúÿÿÿÿÿÿÿÿÿ¿Ÿþ¿ÿëþ¿¾+ê󪿺ûÿÿ¿»ÿÿþ¿êÿÿªûÿÿÿÿÿºûÿÿ¿»ÿÿþ¿mÿÿÿýÿÿÿÿÿ ú¢ª±«¯Žü(:ú¢ÿ¿«¯Žü(:ú¢ÿ¿«¯Žü(:ú¢ÿ¿«¯Žü( \ 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 -CH18623 NA18623 0 0 1 1 -CH18576 NA18576 0 0 2 1 -CH18577 NA18577 0 0 2 1 -CH18624 NA18624 0 0 1 1 -CH18579 NA18579 0 0 2 1 -CH18632 NA18632 0 0 1 2 -CH18582 NA18582 0 0 2 1 -CH18633 NA18633 0 0 1 1 -CH18635 NA18635 0 0 1 2 -CH18592 NA18592 0 0 2 1 -CH18636 NA18636 0 0 1 1 -CH18593 NA18593 0 0 2 2 -CH18637 NA18637 0 0 1 1 -JA18942 NA18942 0 0 2 2 -JA18940 NA18940 0 0 1 2 -JA18951 NA18951 0 0 2 2 -JA18943 NA18943 0 0 1 2 -JA18947 NA18947 0 0 2 2 -JA18944 NA18944 0 0 1 2 -JA18945 NA18945 0 0 1 2 -JA18949 NA18949 0 0 2 2 -JA18948 NA18948 0 0 1 2 -JA18952 NA18952 0 0 1 2 -JA18956 NA18956 0 0 2 2 -JA18964 NA18964 0 0 2 2 -JA18953 NA18953 0 0 1 1 -JA18968 NA18968 0 0 2 2 -JA18959 NA18959 0 0 1 2 -JA18969 NA18969 0 0 2 1 -JA18960 NA18960 0 0 1 2 -JA18961 NA18961 0 0 1 2 -JA18972 NA18972 0 0 2 2 -JA18965 NA18965 0 0 1 2 -JA18973 NA18973 0 0 2 2 -JA18966 NA18966 0 0 1 2 -JA18975 NA18975 0 0 2 2 -JA18967 NA18967 0 0 1 2 -JA18976 NA18976 0 0 2 1 -JA18978 NA18978 0 0 2 2 -JA18970 NA18970 0 0 1 1 -JA18980 NA18980 0 0 2 2 -JA18995 NA18995 0 0 1 1 -JA18981 NA18981 0 0 2 2 -JA18971 NA18971 0 0 1 2 -JA18974 NA18974 0 0 1 1 -JA18987 NA18987 0 0 2 2 -JA18990 NA18990 0 0 1 1 -JA18991 NA18991 0 0 2 2 -JA18994 NA18994 0 0 1 2 -JA18992 NA18992 0 0 2 2 -JA18997 NA18997 0 0 2 2 -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 -CH18524 NA18524 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -CH18529 NA18529 0 0 2 1 C C A A T C A G T C T C T C C C G A G C -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 -CH18542 NA18542 0 0 2 1 C C G A T C G G C C C C C C C C A A C C -CH18545 NA18545 0 0 2 1 C C G A T C A G T C C C T C C C G A G C -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 -CH18547 NA18547 0 0 2 2 C C G A T C A G T C C C T C C C G A G C -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 -CH18552 NA18552 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18611 NA18611 0 0 1 1 C C G A T C A G T C C C T C C C G A G C -CH18555 NA18555 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18564 NA18564 0 0 2 2 C C A A T C G G C C C C C C C C A A C C -CH18566 NA18566 0 0 2 1 C C A A T C A G C C C C C C T C A A C C -CH18563 NA18563 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -CH18570 NA18570 0 0 2 1 C C A A T C A G T C T C T C C C G A G C -CH18612 NA18612 0 0 1 2 C C A A T C A A T C T C T C C C G A G C -CH18571 NA18571 0 0 2 1 C C A A T C A G C C C C C C C C A A C C -CH18620 NA18620 0 0 1 1 C C A A C C G G T C T C T C C C G A G C -CH18621 NA18621 0 0 1 1 C C G G T T A A T C C C T C C C G A G C -CH18594 NA18594 0 0 2 1 C C A A T T A A C C C C C C C C A A G C -CH18622 NA18622 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -CH18573 NA18573 0 0 2 2 C C A A T C A G C C 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