[Patchwork-commits] r178 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/patchwork/R pkg/patchwork/inst/perl
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jun 24 14:33:06 CEST 2013
Author: sebastian_d
Date: 2013-06-24 14:33:05 +0200 (Mon, 24 Jun 2013)
New Revision: 178
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.alleledata.r
pkg/patchwork/inst/perl/mpile2alleles.pl
Log:
buggfix for mpilup and patchwork.alleledata
Modified: .git/COMMIT_EDITMSG
===================================================================
--- .git/COMMIT_EDITMSG 2013-06-24 12:07:52 UTC (rev 177)
+++ .git/COMMIT_EDITMSG 2013-06-24 12:33:05 UTC (rev 178)
@@ -1 +1 @@
-Fix for library loading in TAPS
+buggfix for mpilup and patchwork.alleledata
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2013-06-24 12:07:52 UTC (rev 177)
+++ .git/logs/HEAD 2013-06-24 12:33:05 UTC (rev 178)
@@ -48,3 +48,6 @@
b6c91dc80295b120969877f8e582708fb89038cc 532c860ab5cdbc3cbfd3537ef8fe60f35d4935de Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371462084 +0200 pull : Merge made by recursive.
532c860ab5cdbc3cbfd3537ef8fe60f35d4935de 8fa9d868a51e8b4bdee100d16c6219d2541df0a6 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371566516 +0200 commit: Substantial changes to homepage which now incudes TAPS tutorial as well as some changes to TAPS
8fa9d868a51e8b4bdee100d16c6219d2541df0a6 49637041dfcf47c07ecaa49251071ba4e2ad377a Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371633024 +0200 commit: Fix for library loading in TAPS
+49637041dfcf47c07ecaa49251071ba4e2ad377a 85bd8859e23a1fd9cc13dca12d161787786508c9 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371644646 +0200 commit: hopefully fixes to mpile2alleles
+85bd8859e23a1fd9cc13dca12d161787786508c9 86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371719448 +0200 commit: Another fix to mpileup. Time for a QA
+86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372076903 +0200 commit: small change to alleledata to fix HG check.
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2013-06-24 12:07:52 UTC (rev 177)
+++ .git/logs/refs/heads/master 2013-06-24 12:33:05 UTC (rev 178)
@@ -48,3 +48,6 @@
b6c91dc80295b120969877f8e582708fb89038cc 532c860ab5cdbc3cbfd3537ef8fe60f35d4935de Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371462084 +0200 pull : Merge made by recursive.
532c860ab5cdbc3cbfd3537ef8fe60f35d4935de 8fa9d868a51e8b4bdee100d16c6219d2541df0a6 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371566516 +0200 commit: Substantial changes to homepage which now incudes TAPS tutorial as well as some changes to TAPS
8fa9d868a51e8b4bdee100d16c6219d2541df0a6 49637041dfcf47c07ecaa49251071ba4e2ad377a Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371633024 +0200 commit: Fix for library loading in TAPS
+49637041dfcf47c07ecaa49251071ba4e2ad377a 85bd8859e23a1fd9cc13dca12d161787786508c9 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371644646 +0200 commit: hopefully fixes to mpile2alleles
+85bd8859e23a1fd9cc13dca12d161787786508c9 86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371719448 +0200 commit: Another fix to mpileup. Time for a QA
+86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372076903 +0200 commit: small change to alleledata to fix HG check.
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2013-06-24 12:07:52 UTC (rev 177)
+++ .git/logs/refs/remotes/origin/master 2013-06-24 12:33:05 UTC (rev 178)
@@ -46,3 +46,6 @@
5eeba51632467a2cf6300bb53b26c98e0a03d735 6eb4b7b50b8a1e1e97b2abc30404fa09d78e029e Sebastian DiLorenzo <S_D at imv096.medsci.uu.se> 1371461678 +0200 pull : fast-forward
6eb4b7b50b8a1e1e97b2abc30404fa09d78e029e 8fa9d868a51e8b4bdee100d16c6219d2541df0a6 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371566540 +0200 update by push
8fa9d868a51e8b4bdee100d16c6219d2541df0a6 49637041dfcf47c07ecaa49251071ba4e2ad377a Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371633040 +0200 update by push
+49637041dfcf47c07ecaa49251071ba4e2ad377a 85bd8859e23a1fd9cc13dca12d161787786508c9 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371644659 +0200 update by push
+85bd8859e23a1fd9cc13dca12d161787786508c9 86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371719471 +0200 update by push
+86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372076931 +0200 update by push
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2013-06-24 12:07:52 UTC (rev 177)
+++ .git/refs/heads/master 2013-06-24 12:33:05 UTC (rev 178)
@@ -1 +1 @@
-49637041dfcf47c07ecaa49251071ba4e2ad377a
+5a0091d4eaca40691cb6bc59d83f9d1ab55f8566
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2013-06-24 12:07:52 UTC (rev 177)
+++ .git/refs/remotes/origin/master 2013-06-24 12:33:05 UTC (rev 178)
@@ -1 +1 @@
-49637041dfcf47c07ecaa49251071ba4e2ad377a
+5a0091d4eaca40691cb6bc59d83f9d1ab55f8566
Modified: pkg/patchwork/R/patchwork.alleledata.r
===================================================================
--- pkg/patchwork/R/patchwork.alleledata.r 2013-06-24 12:07:52 UTC (rev 177)
+++ pkg/patchwork/R/patchwork.alleledata.r 2013-06-24 12:33:05 UTC (rev 178)
@@ -74,7 +74,8 @@
hgcheck = strsplit(line,"\t")
#Sometimes chr1 isnt first in the pileup file, traverse until you get to chr1 to see if hg18 or hg19 should be applied.
- while((hgcheck[[1]][1] != "chr1") || (hgcheck[[1]][1] != "1"))
+ #while hgcheck is not "chr1" AND not "1"
+ while((hgcheck[[1]][1] != "chr1") && (hgcheck[[1]][1] != "1"))
{
line = readLines(con,1)
hgcheck = strsplit(line,"\t")
Modified: pkg/patchwork/inst/perl/mpile2alleles.pl
===================================================================
--- pkg/patchwork/inst/perl/mpile2alleles.pl 2013-06-24 12:07:52 UTC (rev 177)
+++ pkg/patchwork/inst/perl/mpile2alleles.pl 2013-06-24 12:33:05 UTC (rev 178)
@@ -14,6 +14,12 @@
open(PILEUP,$ARGV[0]) or die "Could not read from $ARGV[0] , stopping.";
open(VCF,$ARGV[1]) or die "Could not read from $ARGV[1] , stopping.";
+#For testing purposes
+#OUT shows faulty lines and the values they are given
+#OK shows a bunch of OK lines to compare too.
+# open(OUT,">out.txt");
+# open(OK,">OK.txt");
+
my %snps;
my %iupac;
$iupac{'A'}{'R'} = 'G';
@@ -41,30 +47,67 @@
$iupac{'T'}{'S'} = 'G|C';
$iupac{'T'}{'M'} = 'A|C';
+#For testing purposes
+# my $i = 0;
+# my $j = 0;
+#perl mpile2alleles.pl SRR389821.mpileup SRR389821.vcf > test.out
+
while (<VCF>)
{
chomp;
next if /^#/;
my ($vchr, $vpos, $cons, $consQual) = (split /\t/, $_)[0,1,4,5];
+ next if $cons eq 'N';
+ next if length $cons > 1;
+ $cons = uc $cons;
+
while (<PILEUP>)
{
chomp;
my ($chr, $pos, $ref, $depth, $baseString) = (split /\t/, $_)[0,1,2,3,4];
+ #For testing purposes
+ # $j++;
+
+ #uc upper case
+ $ref = uc $ref;
+ next if $ref eq '*';
+
#If the position and chromosome match between pileup and vcf
# add if smaller than
if ($vchr eq $chr && $vpos == $pos)
{
- $ref = uc $ref;
- next if $ref eq '*';
- next if $cons eq 'N';
my $snp = ($cons =~ m/[AGCT]/) ? $cons : $iupac{$ref}{$cons};
$snps{$chr}{$pos}{'ref'} = $ref;
$snps{$chr}{$pos}{'snp'} = $snp;
$snps{$chr}{$pos}{'qual'} = $consQual;
+ # #For testing purposes
+ # $j == the faulty line number so we can see what is actually happening there
+ # if($j == 576673 || $j == 683784 || $j == 733447)
+ # {
+ # print OUT "Line: $. \n";
+ # print OUT "VCF: $vchr $vpos $cons $consQual \n";
+ # print OUT "PILEUP: $chr $pos $ref $depth $baseString \n";
+ # print OUT "snp: $snp \n";
+ # print OUT "assigned: $snps{$chr}{$pos}{'snp'} \n";
+ # $i++;
+ # }
+
+ # print OK "Line: $. \n";
+ # print OK "VCF: $vchr $vpos $cons $consQual \n";
+ # print OK "PILEUP: $chr $pos $ref $depth $baseString \n";
+ # print OK "snp: $snp \n";
+ # print OK "assigned: $snps{$chr}{$pos}{'snp'} \n";
+
+ # if ($i == 3)
+ # {
+ # close(OUT);
+ # close(OK);
+ # }
+
my $snpCount;
if ($snps{$chr}{$pos}{'snp'} eq 'A') {
$snpCount = $baseString =~ tr/Aa/Aa/;
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