finding pattern takes one mismatch

sdparekh · Jan 17, 2019 · 6b5cb07 · 6b5cb07
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diff --git a/Approx.pm b/Approx.pm
diff --git a/ExampleData/Example.BCstats.txt b/ExampleData/Example.BCstats.txt
diff --git a/ExampleData/Example.filtered.tagged.Log.final.out b/ExampleData/Example.filtered.tagged.Log.final.out
diff --git a/ExampleData/Example.filtered.tagged.Log.out b/ExampleData/Example.filtered.tagged.Log.out
diff --git a/ExampleData/Example.filtered.tagged.Log.progress.out b/ExampleData/Example.filtered.tagged.Log.progress.out
diff --git a/ExampleData/Example.filtered.tagged.SJ.out.tab b/ExampleData/Example.filtered.tagged.SJ.out.tab
diff --git a/ExampleData/Example.nohup.out b/ExampleData/Example.nohup.out
diff --git a/ExampleData/Example.postmap.yaml b/ExampleData/Example.postmap.yaml
diff --git a/ExampleData/Example.yaml b/ExampleData/Example.yaml
diff --git a/ExampleData/zUMIs_output/.currentRGgroup.txt b/ExampleData/zUMIs_output/.currentRGgroup.txt
diff --git a/ExampleData/zUMIs_output/Examplekept_barcodes.txt b/ExampleData/zUMIs_output/Examplekept_barcodes.txt
diff --git a/ExampleData/zUMIs_output/expression/Example.dgecounts.rds b/ExampleData/zUMIs_output/expression/Example.dgecounts.rds
diff --git a/ExampleData/zUMIs_output/stats/Example.UMIcounts.txt b/ExampleData/zUMIs_output/stats/Example.UMIcounts.txt
diff --git a/ExampleData/zUMIs_output/stats/Example.bc.READcounts.rds b/ExampleData/zUMIs_output/stats/Example.bc.READcounts.rds
diff --git a/ExampleData/zUMIs_output/stats/Example.detected_cells.pdf b/ExampleData/zUMIs_output/stats/Example.detected_cells.pdf
diff --git a/ExampleData/zUMIs_output/stats/Example.downsampling_thresholds.pdf b/ExampleData/zUMIs_output/stats/Example.downsampling_thresholds.pdf
diff --git a/ExampleData/zUMIs_output/stats/Example.features.pdf b/ExampleData/zUMIs_output/stats/Example.features.pdf
diff --git a/ExampleData/zUMIs_output/stats/Example.geneUMIcounts.pdf b/ExampleData/zUMIs_output/stats/Example.geneUMIcounts.pdf
diff --git a/ExampleData/zUMIs_output/stats/Example.genecounts.txt b/ExampleData/zUMIs_output/stats/Example.genecounts.txt
diff --git a/ExampleData/zUMIs_output/stats/Example.readspercell.pdf b/ExampleData/zUMIs_output/stats/Example.readspercell.pdf
diff --git a/ExampleData/zUMIs_output/stats/Example.readspercell.txt b/ExampleData/zUMIs_output/stats/Example.readspercell.txt
diff --git a/ExampleData/zUMIs_runlog.txt b/ExampleData/zUMIs_runlog.txt
diff --git a/README.md b/README.md
@@ -25,6 +25,9 @@ The previous implementation of zUMIs has moved to an [archive branch in GitHub](
 
 
 ## Changelog
+17 Jan 2019: [zUMIs2.2.3 released] (https://github.com/sdparekh/zUMIs/releases/tag/zUMIs2.2.3).
+We implemented fuzzy matching for pattern finding. From this version onwards, finding patterns take one mismatch into account.
+
 14 Oct 2018: [zUMIs2.2 released](https://github.com/sdparekh/zUMIs/releases/tag/zUMIs2.2).
 Since the big update of zUMIs2, we have continuously improved performance and fixed bugs. Additionally, we have implemented a barcode-frameshift correction, which helps for [ddSeq/Surecell data](https://github.com/sdparekh/zUMIs/wiki/Protocol-specific-setup#ddseq--surecell-3).
 

diff --git a/fqfilter_v2.pl b/fqfilter_v2.pl
@@ -21,6 +21,7 @@ BEGIN
 }
 use lib "$zumisdir";
 use distilReads;
+use Approx;
 
 open(YL,"$rscriptexc $zumisdir/readYaml4fqfilter.R $yml |");
 @arg=<YL>;
@@ -218,7 +219,8 @@ BEGIN
     $mtmp = grep {$_ < $umithres[1]} @mquals;
 
     # print out only if above the quality threshold
-    if(($btmp < $bcthres[0]) && ($mtmp < $umithres[0]) && ($mcrseq =~ m/^$checkpattern/) && ($isPass ne "fail")){
+     if(($btmp < $bcthres[0]) && ($mtmp < $umithres[0]) && ( Approx::amatch($checkpattern, [ 1 ],$mcrseq) ) && ($isPass ne "fail")){
+	     #if(($btmp < $bcthres[0]) && ($mtmp < $umithres[0]) && ($mcrseq =~ m/^$checkpattern/) && ($isPass ne "fail")){
     #if(($btmp < $bcthres[0]) && ($mtmp < $umithres[0])){
 
       chomp($rid);

diff --git a/zUMIs-master.sh b/zUMIs-master.sh
@@ -3,7 +3,7 @@
 # Pipeline to run UMI-seq analysis from fastq to read count tables.
 # Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann
 # Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se
-vers=2.2.2c
+vers=2.2.3
 currentv=`curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/master/zUMIs-master.sh | grep '^vers=' | cut -f2 -d "="`
 if [ "$currentv" != "$vers" ]; then echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------"; fi