V1.1.1

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2017 Le LI
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,8 +1,17 @@
+# Updates in May31, 2018:
+=================================================================================
+Added a low-coverage mode in the pipeline to support the cases that the input alignment is low-coverage (e.g. <10x for the alignment of consensus maps to the reference). 
+
+To trigger this mode, please set 
++	"likelihoodRatioCutOff" as 0, 
++	"numberOfSupportIndelMolecule" as 1. 
+
+=================================================================================
 # OMSV TUTORIAL
 =================================================================================
 ## Overall
 Here we provide the package of OMSV with all source codes (C++, bash script, and Matlab codes) and binary files. The scrips of OMSV have been tested in Debian GNU/Linux 9.0 (stretch) and CentOS Linux release 7.3.1611 (Core) platform and the matlab code was developed in Matlab R2011b (7.13.0.564) 64-bit (glnxa64). The way to start our pipeline within a few steps and the details of the programs, including input parameters and supported file formats, are shown in "Readme\_OMSV.txt".  
-**All data** (raw optical mapping data and alignments) are accessible at [here](https://drive.google.com/drive/folders/0B4T3OTv54s2DbDdLRFdqdERXZkE). The alignment file, as well as the 2-round split alignment, of NA12878 are provided for the quick start. 
+**All data** (raw optical mapping data and alignments) are accessible at [Zenodo repository](https://doi.org/10.5281/zenodo.886387). The alignment file, as well as the 2-round split alignment, of NA12878 are provided for the quick start. 
 
 =================================================================================
 ## Quick Start
@@ -14,14 +23,14 @@ To quickly try our OMSV Caller, please first download the package and alignment
 >cd OMSV  
 >chmod 777 makefile  
 >./makefile  
->./callSV.sh (Run the original version, of which the results are consistent with the published results)
+>./callSV.sh (Run the latest version, of which the results should be slightly different)
 
-callSV\_old.sh (callSV.sh) provide the examples of calling the OMSV callers (Matlab is required to call CNVs). Then you can find the resulting lists in SV\_result with prefix 12878 (e.g. 12878Indel.osv, 12878Mixed\_indel.osv, and 12878Complex\_total.bed).
+callSV.sh provide the examples of calling the OMSV callers (Matlab is required to call CNVs). Then you can find the resulting lists in SV\_result with prefix 12878 (e.g. 12878Indel.osv, 12878Mixed\_indel.osv, and 12878Complex\_total.bed).
 
 =================================================================================
 ## Parameters and Settings of the tools:  
 
-+ OMSV/OMSV\_mixedIndel (type ./OMSV to check the parameters) to call indels and mixed indels and site variations:  
++ OMSV (type ./OMSV to check the parameters) to call indels and mixed indels and site variations:  
 	- -inputLabel:  Default value: 878. The index/label of genome.  
 	- -outputFolder:	Default value: ./. The path of the folder to store the output fils.
 	- -SVoutputFile:	Default value: Detected_structual_variants. The prefix of the file name of SVs (.osv).
@@ -74,4 +83,4 @@ callSV\_old.sh (callSV.sh) provide the examples of calling the OMSV callers (Mat
 
 =================================================================================
 ## Citation:
-> Le Li, Tsz-Piu Kwok, Alden King-Yung Leung, et.al. **OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps**. *Manuscript under revision, 2017*.
+> Le Li, Tsz-Piu Kwok, Alden King-Yung Leung, et.al. **OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps**. *Genome biology, 2017, 18(1): 230*.

callSV.sh

@@ -7,27 +7,26 @@ fi
 if [ $step -lt 1 ]
 then
 
-echo "1. Start to call large indels"
+echo "1. Start to call large indels and site of NA12878"
 mkdir temp
+
 ./OMSV -inputLabel 12878 -outputFolder SV_result/ -SVoutputFile Indel -chrMapFile hg38_r.cmap -optAlignFile data/NA12878_700bp_hg38_combRefOMB2.oma -optTempFolder temp/
-rm -f SV_result/*_List.txt
-./postFilter.sh SV_result/12878Indel_2000.osv 2000
 
-echo "2. Start to call mixed indels"
-./OMSV_mixedIndel -inputLabel 12878 -outputFolder SV_result/ -SVoutputFile Mixed_indel -chrMapFile hg38_r.cmap -optAlignFile data/NA12878_700bp_hg38_combRefOMB2.oma -optTempFolder temp/
-rm -f SV_result/*_List.txt
-./postFilter.sh SV_result/12878Mixed_indel_2000.osv 2000
-sed '/Homozygous/d' SV_result/12878Mixed_indel_2000.osv | sed '/Heterozygous/d' > SV_result/12878Mixed_indel_2000.osv_tp && mv SV_result/12878Mixed_indel_2000.osv_tp SV_result/12878Mixed_indel_2000.osv
+sed '/.site\|#/!d' SV_result/12878Indel_2000.osv > SV_result/12878Sites_2000.osv
+sed '/Homozygous\|Heterozygous/d' SV_result/12878Indel_2000.osv > SV_result/12878Mixed_indel_2000.osv
+sed -i '/.site\|HDI\|HI1I2\|HD1D2/d' SV_result/12878Indel_2000.osv
 
+rm -f SV_result/*_List.txt
+./postFilter.sh SV_result/12878Indel_2000.osv 2000
 
 rm -r -f temp
 fi
 
 echo "2. Start to call medium-size inversions"
-if java -jar OMTools-master/OMTools.jar >/dev/null 2>&1
+if java -jar */OMTools.jar >/dev/null 2>&1
 then
 
-	java -jar OMTools/OMTools.jar SVDetection --refmapin hg38_r.cmap --optresin data/NA12878_700bp_hg38_combRefOMB2.oma --mininvsig 4 --svout 12878Med_inv.osv --flanksig 0 --deg 0 -svmode 2 -minsupport 10 && sed -i '/.site/d' 12878Med_inv.osv
+	java -jar */OMTools.jar SVDetection --refmapin hg38_r.cmap --optresin data/NA12878_700bp_hg38_combRefOMB2.oma --mininvsig 4 --svout 12878Med_inv.osv --flanksig 0 --deg 0 -svmode 2 -minsupport 10 && sed -i '/.site/d' 12878Med_inv.osv
 else
         echo "Medium-size inversion caller requires java and OMTools but not installed. Skip this step."
 fi

makefile

@@ -1,5 +1,4 @@
-g++ -std=c++11 source/OMSV_v3.cpp -o OMSV
-g++ -std=c++11 source/OMSV_mixedIndel_v3.cpp -o OMSV_mixedIndel
+g++ -std=c++11 source/OMSV_v4.cpp -o OMSV
 g++ -std=c++11 source/filterSV.cpp -o filterSV
 g++ -std=c++11 source/adjust_split.cpp -o adjust_split
 g++ -std=c++11 source/breakpoint.cpp -o breakpoint