deprecated refilter and updated verison number

README.md

@@ -12,7 +12,7 @@ Table of contents
   * [Installation](#gh-md-toc)
   * [Description](#description)
   * [Output file description](#output-file-description)
-  * [Filtering and refiltering](#filtering-and-refiltering)
+  * [Filtering](#filtering-and-refiltering)
   * [Recipes and examples](#recipes-and-examples)
     * [Whole genome somatic SV and indel detection](#whole-genome-somatic-sv-and-indel-detection)
     * [Whole genome germline SV and indel detection](#whole-genome-germline-sv-and-indel-detection)
@@ -75,8 +75,7 @@ Output file description
 -----------------------
 
 ##### ``*.bps.txt.gz``
-Raw, unfiltered variants. This file is parsed at the end to produce the VCF files. With the bps.txt.gz,
-one can define a new set of filteirng criteria (depending on sensitivity/specificity needs) using ``svaba refilter``. 
+Raw, unfiltered variants. This file is parsed at the end to produce the VCF files. 
 
 ##### ``*.contigs.bam``
 All assembly contigs as aligned to the reference with BWA-MEM. Note that this is an unsorted file. To view in IGV,
@@ -105,7 +104,7 @@ the cutoff for rearrangement vs indel is taken from BWA-MEM, whether it produces
 or two separate alignments. This is an arbitrary cutoff, just as there is no clear consensus distinction between what 
 constitutes an "indel" and a "structural variant". The unfiltered VCF files include non-PASS variants. 
 
-Filtering and Refiltering
+Filtering
 -----------------------
 
 SvABA performs a series of log-likelihood calculations for each variant. The purpose is to first classify a variant as real vs artifact, 
@@ -114,9 +113,6 @@ and then to determine if the variant is somatic or germline. These log-likelihoo
 * ``LR`` - Log of the odds that the variant has allelic fraction (AF) of 0 or >=0.5. This is used for somatic vs germline classification
 * ``SL`` - Scaled LOD. LOD scores is heuristically scaled as: (min(Mapping quality #1, Mapping quality #2) - 2 * NM) / 60 * LOD
 
-SvABA can refilter the bps.txt.gz file to produce new VCFs with different stringency cutoffs. To run, the following are required:
-* ``-b`` - a BAM from the original run, which is used just for its header
-* ``-i`` - input bps.txt.gz file
 
 Examples and recipes
 --------------------

src/svaba/run_svaba.h

@@ -24,7 +24,7 @@
 
 #include "workqueue.h"
 
-#define SVABA_VERSION "1.1.3"
+#define SVABA_VERSION "1.2.0"
 
 // typedefs
 typedef std::map<std::string, std::string> BamMap;

src/svaba/svaba.cpp

@@ -24,7 +24,6 @@ static const char *SVABA_USAGE_MESSAGE =
 "Usage: svaba <command> [options]\n\n"
 "Commands:\n"
 "           run            Run SvABA SV and Indel detection on BAM(s)\n"
-"           refilter       Refilter the SvABA breakpoints with additional/different criteria to created filtered VCF and breakpoints file.\n"
 "\nReport bugs to [email protected] \n\n";
 
 int main(int argc, char** argv) {
@@ -39,10 +38,9 @@ int main(int argc, char** argv) {
       return 0;
     } else if (command == "run") {
       runsvaba(argc -1, argv + 1);
-    } else if (command == "refilter") {
-      runRefilterBreakpoints(argc-1, argv+1);
-    }
-    else {
+      /*    } else if (command == "refilter") {
+	    runRefilterBreakpoints(argc-1, argv+1); */
+    } else {
       std::cerr << SVABA_USAGE_MESSAGE;
       return 0;
     }