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Update annotSeg_7102f1c.pl #471

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Update annotSeg_7102f1c.pl #471

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11657b1
Merge pull request #374 from tgen/potential-lancet-changes
PedalheadPHX Aug 27, 2020
460d92d
Merge pull request #379 from tgen/develop
Sep 4, 2020
66f976a
Update pipeline.yaml
bryce-turner Sep 4, 2020
815c0ce
Merge pull request #380 from tgen/master_versioning
Sep 4, 2020
797f418
Merge pull request #401 from tgen/develop
Feb 4, 2021
f26d5b6
Increment pipeline version
bryce-turner Feb 4, 2021
436aae1
Merge pull request #402 from tgen/release_v1.1.0_versioning
Feb 4, 2021
c99cc7c
Merge pull request #405 from tgen/develop
Feb 9, 2021
ae50e17
Merge pull request #409 from tgen/develop
Mar 12, 2021
30d834d
Pipeline version bump for v1.1.1
bryce-turner Mar 12, 2021
7277064
Merge pull request #410 from tgen/pipeline_versioning_v1_1_1
Mar 12, 2021
b419386
Merge pull request #412 from tgen/develop
PedalheadPHX Mar 17, 2021
ace7746
Update pipeline.yaml
bryce-turner Mar 17, 2021
281cb80
Merge pull request #413 from tgen/v1.1.2-versioning
PedalheadPHX Mar 17, 2021
84d1ddf
Merge pull request #446 from tgen/develop
PedalheadPHX Aug 4, 2021
2834c7b
Update pipeline.yaml
bryce-turner Aug 4, 2021
0fc0c06
Update pipeline.yaml
bryce-turner Aug 4, 2021
9f04da2
Merge pull request #449 from tgen/release_v1.2_versioning
PedalheadPHX Aug 4, 2021
854dced
Update annotSeg_7102f1c.pl
tizatt Sep 26, 2022
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2 changes: 1 addition & 1 deletion pipeline.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ __pipeline__:
name: phoenix
main: main.jst
description: Human GRCh38 genomics suite
version: development
version: v1.2.0
constants:
tools:
bedtools:
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9 changes: 6 additions & 3 deletions required_scripts/annotSeg_7102f1c.pl
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Expand Up @@ -64,10 +64,13 @@

my %gene;
foreach my $k (keys %geneA){
$st=int($loc{$k}/100);
$en=int($loc2{$k}/100);
$st1=int($loc{$k}-100);
$st=int($st1/100);
$en1=int($loc{$k}+100);
$en=int($en1/100);

if ($st>$en) {$t=$en;$en=$st;$st=$t;}
for ($i=$st-100;$i<=$en+100;++$i*100) {
for ($i=$st;$i<=$en;++$i*100) {
if ($chr{$k} eq "X") {$chr{$k}=23;}
if ($chr{$k} eq "Y") {$chr{$k}=24;}
if (exists($gene{"$chr{$k}_$i"})) {
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