From 25537576d9291aecfdfbcd2338e2f6e0323524f0 Mon Sep 17 00:00:00 2001
From: tobiasrausch <rauschtobi@gmail.com>
Date: Fri, 6 Mar 2020 11:01:42 +0100
Subject: [PATCH] v0.2.3

---
 README.md     | 24 ++++++++++++++++++++----
 src/version.h |  2 +-
 2 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 578c292..4fec4d6 100644
--- a/README.md
+++ b/README.md
@@ -27,15 +27,31 @@ Download the 1000 Genomes k-mer maps here: [http://gear.embl.de/data/rdxon/](htt
 
 To filter an input FASTQ file against the 1000 Genomes sequencing data simply run
 
-`./src/rdxon filter -x kmer.x.map -y kmer.y.map -o <output.fq.gz> <input.fq.gz>`
+`rdxon filter -x kmer.x.map -y kmer.y.map -o <output.fq.gz> <input.fq.gz>`
 
 You can also dump all rare k-mers which are absent in 1000 Genomes to a file
 
-`./src/rdxon filter -x kmer.x.map -y kmer.y.map -u <kmer.gz> -o <output.fq.gz> <input.fq.gz>`
+`rdxon filter -x kmer.x.map -y kmer.y.map -u <kmer.gz> -o <output.fq.gz> <input.fq.gz>`
 
-For paired-end data you can run Read1 and Read2 in parallel and then concatenate the output FASTQ files. For downstream analysis, you should always use the output FASTQ file as a single-end dataset.
+For paired-end data you can run Read1 and Read2 in parallel and then concatenate the output FASTQ files.
 
-# Approximate runtime and memory usage
+# Paired-end mode
+
+For certain downstream applications, you may want to retain proper paired-ends.
+
+`rdxon filter -x kmer.x.map -y kmer.y.map -o <outprefix> <read1.fq.gz> <read2.fq.gz>`
+
+# Rare and somatic k-mers
+
+For tumor-normal sequencing in cancer genomics, you can also filter for reads that contain rare and somatic k-mers.
+
+`rdxon somatic -x kmer.x.map -y kmer.y.map -o <output.fq.gz> <tumor.fq.gz> <control.fq.gz>`
+
+The somatic subcommand is also available in paired-end mode.
+
+`rdxon somatic -x kmer.x.map -y kmer.y.map -o <outprefix> <tumor.1.fq.gz> <tumor.2.fq.gz> <control.1.fq.gz> <control.2.fq.gz>`
+
+# Approximate runtime and memory usage for filtering reads containing rare k-mers
 
 Whole-exome sequencing: ~1 hour and ~4G RAM (single CPU, one job for Read1 and Read2)
 
diff --git a/src/version.h b/src/version.h
index 89a4740..28617aa 100644
--- a/src/version.h
+++ b/src/version.h
@@ -5,7 +5,7 @@ namespace rdxon
 {
 
 
-  std::string rdxonVersionNumber = "0.1.2";
+  std::string rdxonVersionNumber = "0.2.3";
 
   inline 
     void printTitle(std::string const& title)