Commits · a74b814509d7ea9122b4cc0d65d501ff54b0cc5e · violethaze74 / Artemis

Dec 13, 2010

change to 2011 · a74b8145

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15225 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a74b8145

Dec 09, 2010

determine if BCF is VCF v4 using the header · c56f05ea

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15215 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c56f05ea

move all filters to VCFFilter class · c205c08f

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15214 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c205c08f

Dec 07, 2010

add more filtering · 2655ab05

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15198 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2655ab05

VCF record filtering · 09841c61

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15197 ee4ac58c-ac51-4696-9907-e4b3aa274f04

09841c61

pass VCFRecord in showVariant() and use VCFFilter · 16cc6f22

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15196 ee4ac58c-ac51-4696-9907-e4b3aa274f04

16cc6f22

add getInfoValue() · bef97ebd

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15195 ee4ac58c-ac51-4696-9907-e4b3aa274f04

bef97ebd

check chr in next() and catch exception in looking up offset · 1476ddc3

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15191 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1476ddc3

add VCFview logger · 467385fd

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15185 ee4ac58c-ac51-4696-9907-e4b3aa274f04

467385fd

include values of all sample data · 635d52e3

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15184 ee4ac58c-ac51-4696-9907-e4b3aa274f04

635d52e3

use VCFRecord getters/setters · ec321924

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15181 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ec321924

add getters and setters · ecf815cc

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15180 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ecf815cc

handle export for BCF to VCF · 2e6dedae

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15179 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2e6dedae

Dec 06, 2010

update to v.1.36 · 94735c52

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15176 ee4ac58c-ac51-4696-9907-e4b3aa274f04

94735c52

Dec 05, 2010

add BCF support · 30bc5841

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15174 ee4ac58c-ac51-4696-9907-e4b3aa274f04

30bc5841

update · 67a96ccd

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15173 ee4ac58c-ac51-4696-9907-e4b3aa274f04

67a96ccd

GT print fix · ef9235b7

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15172 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ef9235b7

Dec 04, 2010

handle empty sample data · f72f74ea

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15171 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f72f74ea

allow BCF files to be imported · 0c6b1cb4

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15170 ee4ac58c-ac51-4696-9907-e4b3aa274f04

0c6b1cb4

add BCF reader to VCFview · 634b4b1c

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15169 ee4ac58c-ac51-4696-9907-e4b3aa274f04

634b4b1c

use getNumAlleles() · 528af603

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15168 ee4ac58c-ac51-4696-9907-e4b3aa274f04

528af603

add getNumAlleles() · 4124be61

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15167 ee4ac58c-ac51-4696-9907-e4b3aa274f04

4124be61

use VCFRecord · 199d84b8

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15166 ee4ac58c-ac51-4696-9907-e4b3aa274f04

199d84b8

change parameter name in VCFRecord · 945766fe

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15165 ee4ac58c-ac51-4696-9907-e4b3aa274f04

945766fe

add parse() to create VCFRecord from a VCF line · 2bd6a68f

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15164 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2bd6a68f

store sample data as an array · 8b522570

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15163 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8b522570

assign contents of VCFRecord in getParts() · 9cc478de

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15162 ee4ac58c-ac51-4696-9907-e4b3aa274f04

9cc478de

add filter · 583fc312

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15161 ee4ac58c-ac51-4696-9907-e4b3aa274f04

583fc312

Dec 03, 2010

read header information · 999836a3

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15160 ee4ac58c-ac51-4696-9907-e4b3aa274f04

999836a3

add tag_peptide · f20cd35d

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15159 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f20cd35d

implement next() · c55aeeb5

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15158 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c55aeeb5

VCF record · 61fd7d31

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15157 ee4ac58c-ac51-4696-9907-e4b3aa274f04

61fd7d31

BCF reading · 89169447

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15154 ee4ac58c-ac51-4696-9907-e4b3aa274f04

89169447

Dec 02, 2010

remove classpath echo · 2a5cf1cf

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15149 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2a5cf1cf

add tmRNA · 6d00a729

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15148 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6d00a729

Nov 30, 2010

update · 09f720b8

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15134 ee4ac58c-ac51-4696-9907-e4b3aa274f04

09f720b8

fix rounding error for long sequences on one line · 7f49034c

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15133 ee4ac58c-ac51-4696-9907-e4b3aa274f04

7f49034c

test for BCF file format · a536813c

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15132 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a536813c

add test for BCF file format · b1245134

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15131 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b1245134

Nov 29, 2010

add VCF export option · 8bbbfb8a

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15127 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8bbbfb8a

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