[Patchwork-commits] r162 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/patchwork/R www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Feb 14 11:33:21 CET 2013
Author: sebastian_d
Date: 2013-02-14 11:33:21 +0100 (Thu, 14 Feb 2013)
New Revision: 162
Modified:
.git/COMMIT_EDITMSG
.git/index
.git/logs/HEAD
.git/logs/refs/heads/master
.git/logs/refs/remotes/origin/master
.git/refs/heads/master
.git/refs/remotes/origin/master
pkg/patchwork/R/patchwork.plot.r
www/changelog.php
Log:
Added somatic.Rdata output, also started modifying changelog. Need to change homepage in the future (when we have worked out the kinks) to reflect that patchwork outputs this information
Modified: .git/COMMIT_EDITMSG
===================================================================
--- .git/COMMIT_EDITMSG 2013-02-13 13:14:27 UTC (rev 161)
+++ .git/COMMIT_EDITMSG 2013-02-14 10:33:21 UTC (rev 162)
@@ -1 +1 @@
-Updated error handling in pile2alleles
+Added somatic.Rdata output, also started modifying changelog. Need to change homepage in the future (when we have worked out the kinks) to reflect that patchwork outputs this information
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2013-02-13 13:14:27 UTC (rev 161)
+++ .git/logs/HEAD 2013-02-14 10:33:21 UTC (rev 162)
@@ -30,3 +30,4 @@
4577fee5ce0968b311fa252e9df8fba284522e5d a75b0350402a356de4d9991f66d7fd1bc785a46f Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1359037334 +0100 commit: updates size of cex for karyotype plot to make the small pictures more interpretable
a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1359631509 +0100 commit: removed vercheck as it caused package to fail to build at R-forge
acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1360761388 +0100 commit: Updated error handling in pile2alleles
+f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 ae581e53647259304439e470cd67db340b07cb35 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1360838155 +0100 commit: Added somatic.Rdata output, also started modifying changelog. Need to change homepage in the future (when we have worked out the kinks) to reflect that patchwork outputs this information
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2013-02-13 13:14:27 UTC (rev 161)
+++ .git/logs/refs/heads/master 2013-02-14 10:33:21 UTC (rev 162)
@@ -30,3 +30,4 @@
4577fee5ce0968b311fa252e9df8fba284522e5d a75b0350402a356de4d9991f66d7fd1bc785a46f Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1359037334 +0100 commit: updates size of cex for karyotype plot to make the small pictures more interpretable
a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1359631509 +0100 commit: removed vercheck as it caused package to fail to build at R-forge
acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1360761388 +0100 commit: Updated error handling in pile2alleles
+f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 ae581e53647259304439e470cd67db340b07cb35 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1360838155 +0100 commit: Added somatic.Rdata output, also started modifying changelog. Need to change homepage in the future (when we have worked out the kinks) to reflect that patchwork outputs this information
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2013-02-13 13:14:27 UTC (rev 161)
+++ .git/logs/refs/remotes/origin/master 2013-02-14 10:33:21 UTC (rev 162)
@@ -30,3 +30,4 @@
4577fee5ce0968b311fa252e9df8fba284522e5d a75b0350402a356de4d9991f66d7fd1bc785a46f Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1359037348 +0100 update by push
a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1359631524 +0100 update by push
acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1360761405 +0100 update by push
+f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 ae581e53647259304439e470cd67db340b07cb35 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1360838170 +0100 update by push
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2013-02-13 13:14:27 UTC (rev 161)
+++ .git/refs/heads/master 2013-02-14 10:33:21 UTC (rev 162)
@@ -1 +1 @@
-f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0
+ae581e53647259304439e470cd67db340b07cb35
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2013-02-13 13:14:27 UTC (rev 161)
+++ .git/refs/remotes/origin/master 2013-02-14 10:33:21 UTC (rev 162)
@@ -1 +1 @@
-f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0
+ae581e53647259304439e470cd67db340b07cb35
Modified: pkg/patchwork/R/patchwork.plot.r
===================================================================
--- pkg/patchwork/R/patchwork.plot.r 2013-02-13 13:14:27 UTC (rev 161)
+++ pkg/patchwork/R/patchwork.plot.r 2013-02-14 10:33:21 UTC (rev 162)
@@ -65,6 +65,12 @@
if (!is.null(normalalf))
{
+ ## Extract somatic variants
+ normaltemp=data.frame(achr=normalalf$achr,apos=normalalf$apos,normal=T)
+ somatic <- merge(normaltemp,alf,by=1:2,all.x=F, all.y=T)
+ somatic <- somatic[is.na(somatic$normal),]
+ save(somatic,file=paste(name,"_somatic.Rdata",sep=""))
+ ## Remove all but the heterozygous SNPs
normalalf <- normalalf[normalalf$amin/normalalf$atot > 0.2,]
alf <- merge(normalalf[,1:2],alf,by=1:2,all=F)
}
Modified: www/changelog.php
===================================================================
--- www/changelog.php 2013-02-13 13:14:27 UTC (rev 161)
+++ www/changelog.php 2013-02-14 10:33:21 UTC (rev 162)
@@ -5,6 +5,14 @@
Here you can find the recent changes made to the patchwork and patchworkCG packages.
<br />
+<!-- <hr class="alt1" />
+
+<h5 style="display:inline-block;">patchwork v2.3 - </h5><div style="display:inline-block; width:1px;"></div>
+<h6 style="display:inline-block;">2013</h6>
+<ul>
+ <li>Patchwork now gives you an additional file, <sample_name>_somatic.Rdata, which contains possible, unfiltered, somatic variants.</li>
+</ul> -->
+
<hr class="alt1" />
<h5 style="display:inline-block;">Homepage - </h5><div style="display:inline-block; width:1px;"></div>
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