diff --git a/src/jaccard/jaccardMain.cpp b/src/jaccard/jaccardMain.cpp
index 4e15ffbecd2d0bb8d6fc5fff790e0760fd02f56e..81a626236251d41df29986b39a64959322b8da0f 100644
--- a/src/jaccard/jaccardMain.cpp
+++ b/src/jaccard/jaccardMain.cpp
@@ -64,6 +64,15 @@ void jaccard_help(void) {
cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl;
+ cerr << "\t-s\t" << "Force strandedness. That is, only merge features" << endl;
+ cerr << "\t\tthat are on the same strand." << endl;
+ cerr << "\t\t- By default, merging is done without respect to strand." << endl << endl;
+
+ cerr << "\t-S\t" << "Force merge for one specific strand only." << endl;
+ cerr << "\t\t" << "Follow with + or - to force merge from only" << endl;
+ cerr << "\t\t" << "the forward or reverse strand, respectively." << endl;
+ cerr << "\t\t" << "- By default, merging is done without respect to strand." << endl << endl;
+
cerr << "Notes: " << endl;
cerr << "\t(1) Input files must be sorted by chrom, then start position."
<< endl << endl;
diff --git a/src/mergeFile/mergeMain.cpp b/src/mergeFile/mergeMain.cpp
index 2e74b894ab0de8aa9185945d71e05e4f2e8492de..cf6804e08211b47ffe86fdd42f0ef5a31c378264 100644
--- a/src/mergeFile/mergeMain.cpp
+++ b/src/mergeFile/mergeMain.cpp
@@ -53,13 +53,13 @@ void merge_help(void) {
cerr << "Options: " << endl;
cerr << "\t-s\t" << "Force strandedness. That is, only merge features" << endl;
- cerr << "\t\tthat are the same strand." << endl;
+ cerr << "\t\tthat are on the same strand." << endl;
cerr << "\t\t- By default, merging is done without respect to strand." << endl << endl;
- cerr << "\t-S\t" << "Force mergeing for a _specific_ strand. That is, only merge features" << endl;
- cerr << "\t\tthat from a specific strabd." << endl;
- cerr << "\t\t- For example, -S + will or -S -" << endl;
- cerr << "\t\t- By default, merging is done without respect to strand." << endl << endl;
+ cerr << "\t-S\t" << "Force merge for one specific strand only." << endl;
+ cerr << "\t\t" << "Follow with + or - to force merge from only" << endl;
+ cerr << "\t\t" << "the forward or reverse strand, respectively." << endl;
+ cerr << "\t\t" << "- By default, merging is done without respect to strand." << endl << endl;
cerr << "\t-d\t" << "Maximum distance between features allowed for features" << endl; cerr << "\t\tto be merged." << endl; cerr << "\t\t- Def. 0. That is, overlapping & book-ended features are merged." << endl;
cerr << "\t\t- (INTEGER)" << endl;
diff --git a/src/utils/Contexts/ContextJaccard.cpp b/src/utils/Contexts/ContextJaccard.cpp
index 7dcdda51bbf1bad3f0cce36b0131ee9ea798f80e..24eafbbd2ea0ff1ac5623fdc8463705be97a2593 100644
--- a/src/utils/Contexts/ContextJaccard.cpp
+++ b/src/utils/Contexts/ContextJaccard.cpp
@@ -16,3 +16,94 @@ ContextJaccard::ContextJaccard() {
ContextJaccard::~ContextJaccard() {
}
+
+bool ContextJaccard::parseCmdArgs(int argc, char **argv, int skipFirstArgs)
+{
+ _argc = argc;
+ _argv = argv;
+ _skipFirstArgs = skipFirstArgs;
+ if (_argc < 2) {
+ setShowHelp(true);
+ return false;
+ }
+
+ setProgram(_programNames[argv[0]]);
+
+ _argsProcessed.resize(_argc - _skipFirstArgs, false);
+
+ for (_i=_skipFirstArgs; _i < argc; _i++) {
+ if (isUsed(_i - _skipFirstArgs)) {
+ continue;
+ }
+ else if (strcmp(_argv[_i], "-s") == 0) {
+ if (!handle_s()) return false;
+ }
+ else if (strcmp(_argv[_i], "-S") == 0) {
+ if (!handle_S()) return false;
+ }
+ }
+ return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs);
+}
+
+bool ContextJaccard::isValidState()
+{
+ if (!ContextIntersect::isValidState()) {
+ return false;
+ }
+ // Tests for stranded merge
+ //
+ if (_desiredStrand != FileRecordMergeMgr::ANY_STRAND) { // requested stranded merge
+ for (int i=0; i < getNumInputFiles(); i++) {
+ // make sure file has strand.
+ if (!getFile(i)->recordsHaveStrand()) {
+ _errorMsg = "\n***** ERROR: stranded merge requested, but input file ";
+ _errorMsg += getInputFileName(i);
+ _errorMsg += " does not have strands. *****";
+ return false;
+ }
+ //make sure file is not VCF.
+ if (getFile(1)->getFileType() == FileRecordTypeChecker::VCF_FILE_TYPE) {
+ _errorMsg = "\n***** ERROR: stranded merge not supported for VCF file ";
+ _errorMsg += getInputFileName(i);
+ _errorMsg += ". *****";
+ return false;
+ }
+ }
+ }
+ //column operations not allowed with BAM input
+ if (hasColumnOpsMethods() &&
+ getFile(0)->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
+ _errorMsg = "\n***** ERROR: stranded merge not supported for VCF files. *****";
+ return false;
+ }
+ return true;
+}
+
+bool ContextJaccard::handle_s() {
+ setSameStrand(true);
+ _desiredStrand = FileRecordMergeMgr::SAME_STRAND_EITHER;
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextJaccard::handle_S() {
+ if ((_i+1) < _argc) {
+ bool validChar = false;
+ if (_argv[_i+1][0] == '+') {
+ _desiredStrand = FileRecordMergeMgr::SAME_STRAND_FORWARD;
+ validChar = true;
+ } else if (_argv[_i+1][0] == '-') {
+ validChar = true;
+ _desiredStrand = FileRecordMergeMgr::SAME_STRAND_REVERSE;
+ }
+ if (validChar) {
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ setSameStrand(true);
+ return true;
+ }
+ }
+ _errorMsg = "\n***** ERROR: -S option must be followed by + or -. *****";
+ return false;
+}
diff --git a/src/utils/Contexts/ContextJaccard.h b/src/utils/Contexts/ContextJaccard.h
index 673065dfa84a3e7c54423ac2f92c0b8bd56255db..4cc1671c03373ee3ffe16b43edbade4df03fa912 100644
--- a/src/utils/Contexts/ContextJaccard.h
+++ b/src/utils/Contexts/ContextJaccard.h
@@ -14,10 +14,12 @@ class ContextJaccard : public ContextIntersect {
public:
ContextJaccard();
~ContextJaccard();
+ virtual bool parseCmdArgs(int argc, char **argv, int skipFirstArgs);
+ virtual bool isValidState();
private:
-
-
+ bool handle_s();
+ bool handle_S();
};
#endif /* CONTEXTJACCARD_H_ */
diff --git a/test/jaccard/aMixedStrands.bed b/test/jaccard/aMixedStrands.bed
new file mode 100644
index 0000000000000000000000000000000000000000..b636fcfd87cb667e3affb42f87d932f432e69e30
--- /dev/null
+++ b/test/jaccard/aMixedStrands.bed
@@ -0,0 +1,12 @@
+chr1 10 50 a1f 2 +
+chr1 20 60 b1r 4 -
+chr1 25 70 c1q 8 .
+chr1 30 75 d1q 16 .
+chr1 40 80 e1f 32 +
+chr1 45 90 f1r 64 -
+chr2 10 50 a2q 2 .
+chr2 20 40 b2f 4 +
+chr2 25 50 c2r 8 -
+chr2 30 60 d2f 16 +
+chr2 35 65 e2q 32 .
+chr2 39 80 f2r 64 -
\ No newline at end of file
diff --git a/test/jaccard/bMixedStrands.bed b/test/jaccard/bMixedStrands.bed
new file mode 100644
index 0000000000000000000000000000000000000000..a4ab27fe140534f7bcda6b70bb1469c0dbec20c0
--- /dev/null
+++ b/test/jaccard/bMixedStrands.bed
@@ -0,0 +1,6 @@
+chr1 10 50 2a1r 2 -
+chr1 40 70 2b1q 4 .
+chr1 60 100 2c1f 8 +
+chr2 15 40 2d2f 16 +
+chr2 30 100 2e2r 32 -
+
diff --git a/test/jaccard/test-jaccard.sh b/test/jaccard/test-jaccard.sh
index f979147bde2959de3ea0a8f4b2842d984ab3aa3a..b8d626bd4b50e262dd541ddfc5c90060d5d96296 100644
--- a/test/jaccard/test-jaccard.sh
+++ b/test/jaccard/test-jaccard.sh
@@ -100,3 +100,50 @@ echo \
$BT jaccard -a a.bam -b three_blocks_match.bam > obs
check exp obs
rm exp obs
+
+###########################################################
+# Test jaccard with mixed strand files
+###########################################################
+echo " jaccard.t10...\c"
+echo \
+"intersection union-intersection jaccard n_intersections
+145 180 0.805556 2" >exp
+$BT jaccard -a aMixedStrands.bed -b bMixedStrands.bed > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test jaccard with mixed strand files, -s option
+# (match strand, either forward or reverse)
+###########################################################
+echo " jaccard.t11...\c"
+echo \
+"intersection union-intersection jaccard n_intersections
+120 290 0.413793 4" >exp
+$BT jaccard -a aMixedStrands.bed -b bMixedStrands.bed -s > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test jaccard with mixed strand files, -S + option
+# (match strand, forward only)
+###########################################################
+echo " jaccard.t12...\c"
+echo \
+"intersection union-intersection jaccard n_intersections
+40 135 0.296296 2" >exp
+$BT jaccard -a aMixedStrands.bed -b bMixedStrands.bed -S + > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test jaccard with mixed strand files, -S - option
+# (match strand, reverse only)
+###########################################################
+echo " jaccard.t13...\c"
+echo \
+"intersection union-intersection jaccard n_intersections
+80 155 0.516129 2" > exp
+$BT jaccard -a aMixedStrands.bed -b bMixedStrands.bed -S - > obs
+check obs exp
+rm obs exp
diff --git a/test/jaccard/test-jaccard.sh~ b/test/jaccard/test-jaccard.sh~
deleted file mode 100644
index 9a6526b35ad802f01a58c338e19bc02506e6ab2f..0000000000000000000000000000000000000000
--- a/test/jaccard/test-jaccard.sh~
+++ /dev/null
@@ -1,94 +0,0 @@
-BT=${BT-../../bin/bedtools}
-
-check()
-{
- if diff $1 $2; then
- echo ok
- else
- echo fail
- fi
-}
-
-###########################################################
-# Test a basic self intersection
-###########################################################
-echo " jaccard.t01...\c"
-echo \
-"intersection union-intersection jaccard n_intersections
-110 110 1 2" > exp
-$BT jaccard -a a.bed -b a.bed > obs
-check obs exp
-rm obs exp
-
-
-echo " jaccard.t02...\c"
-echo \
-"intersection union-intersection jaccard n_intersections
-10 140 0.0714286 1" > exp
-$BT jaccard -a a.bed -b b.bed > obs
-check obs exp
-rm obs exp
-
-echo " jaccard.t03...\c"
-echo \
-"intersection union-intersection jaccard n_intersections
-10 200 0.05 1" > exp
-$BT jaccard -a a.bed -b c.bed > obs
-check obs exp
-rm obs exp
-
-
-echo " jaccard.t04...\c"
-echo \
-"intersection union-intersection jaccard n_intersections
-0 210 0 0" > exp
-$BT jaccard -a a.bed -b d.bed > obs
-check obs exp
-rm obs exp
-
-###########################################################
-# Test stdin
-###########################################################
-echo " jaccard.t05...\c"
-echo \
-"intersection union-intersection jaccard n_intersections
-10 140 0.0714286 1" > exp
-cat a.bed | $BT jaccard -a - -b b.bed > obs
-check obs exp
-rm obs exp
-
-
-###########################################################
-# Test symmetry
-###########################################################
-echo " jaccard.t06...\c"
-$BT jaccard -a a.bed -b b.bed > obs1
-$BT jaccard -a b.bed -b a.bed > obs2
-check obs1 obs2
-rm obs1 obs2
-
-###########################################################
-# Test partially matching blocks without -split option.
-###########################################################
-echo " jaccard.t07...\c"
-echo \
-"intersection union-intersection jaccard n_intersections
-10 50 0.2 1" > exp
-$BT jaccard -a three_blocks_match.bed -b e.bed > obs
-check obs exp
-rm obs exp
-
-
-###########################################################
-# Test partially matching blocks with -split option.
-###########################################################
-echo " jaccard.t08...\c"
-echo \
-"intersection union-intersection jaccard n_intersections
-5 55 0.0909091 1" > exp
-$BT jaccard -a three_blocks_match.bed -b e.bed -split > obs
-check obs exp
-rm obs exp
-
-intersection union-intersection jaccard n_intersections
-10 150 0.0666667 1