diff --git a/bin/closestBed b/bin/closestBed
index 53a4cf66b23905c972eee5a5c4758c667239ddcb..63541a904c6d92deb110602434d1ec6a17dfbb69 100755
Binary files a/bin/closestBed and b/bin/closestBed differ
diff --git a/bin/coverageBed b/bin/coverageBed
index d9e498a598659f7ec4ab1b358a75f17922c5db50..3f9086fe300f9409f985f2c0b89f7e01561c096d 100755
Binary files a/bin/coverageBed and b/bin/coverageBed differ
diff --git a/bin/fastaFromBed b/bin/fastaFromBed
index ae02834d47ae5f0e2c5f8156288322cfabf6d9c8..8aefa577fa653ff62f0c633363dd3b09c1760e70 100755
Binary files a/bin/fastaFromBed and b/bin/fastaFromBed differ
diff --git a/bin/genomeCoverageBed b/bin/genomeCoverageBed
index 9fee6e824a8e16e7b428e00c1c7fdb6ac63cefc7..a66cbb8e3abd961f9159dbc75a237e9c09ef0a1b 100755
Binary files a/bin/genomeCoverageBed and b/bin/genomeCoverageBed differ
diff --git a/bin/intersectBed b/bin/intersectBed
index e5d1f914058f9228f40314770b4f79aee16ad8c5..1515cb4d766ef2b11471669b4622cecd25d3bda9 100755
Binary files a/bin/intersectBed and b/bin/intersectBed differ
diff --git a/bin/linksBed b/bin/linksBed
index b72718e947541aaaa44d9ebafafb94e912d2a344..2451430ac77b9b385196e916293c453bf83d4c98 100755
Binary files a/bin/linksBed and b/bin/linksBed differ
diff --git a/bin/maskFastaFromBed b/bin/maskFastaFromBed
index 4ca59c2003448c1d97491daa8e5e3159a3879f02..5a774d031a71ed12bf5b59da6b9da9d779c0d343 100755
Binary files a/bin/maskFastaFromBed and b/bin/maskFastaFromBed differ
diff --git a/bin/mergeBed b/bin/mergeBed
index a6b01aaf7cc4d20728ad88e29ee0c436d242fd65..dc81efa3e271d987a17204cae55f51298e205f87 100755
Binary files a/bin/mergeBed and b/bin/mergeBed differ
diff --git a/bin/shuffleBed b/bin/shuffleBed
index 277c3e97a87112b1d85293a50f48a33363ec1d48..702899588eca18a7ca6453cda295295fc2879b1b 100755
Binary files a/bin/shuffleBed and b/bin/shuffleBed differ
diff --git a/bin/slopBed b/bin/slopBed
index c0f59c82d848c25fdb97d6dee2664dffb7ca8a1d..5d13b256f3cde5ecf9b59c6b4ad6d7155966281b 100755
Binary files a/bin/slopBed and b/bin/slopBed differ
diff --git a/bin/sortBed b/bin/sortBed
index 022c62d4b54c6a84330a8bc5d43ac57645cdd6e1..e4bc89a5cbf4688fb149b8582d9ac0cc0b9e59d0 100755
Binary files a/bin/sortBed and b/bin/sortBed differ
diff --git a/bin/subtractBed b/bin/subtractBed
index eb1e06d8eb7928ada0314489e29277fd6b3431e7..560cddec4a0fe97ae906ecb19fbc1a1510cd1f6e 100755
Binary files a/bin/subtractBed and b/bin/subtractBed differ
diff --git a/bin/windowBed b/bin/windowBed
index c47e3b8c0f9209db30b9819502f7e437f710cfba..a8047ab1f7133f2136476956490a683761d65767 100755
Binary files a/bin/windowBed and b/bin/windowBed differ
diff --git a/obj/closestMain.o b/obj/closestMain.o
index 56671af68b633b23b17381813699f3f07699d1fe..495083760193a0ef651b171572f8acb69b90f127 100644
Binary files a/obj/closestMain.o and b/obj/closestMain.o differ
diff --git a/obj/coverageMain.o b/obj/coverageMain.o
index e7f694a42ae13e1d1f934a5df83b5dc1dd5ab198..3abada83c36e08187f4d1bc9676e90c36284872e 100644
Binary files a/obj/coverageMain.o and b/obj/coverageMain.o differ
diff --git a/obj/fastaFromBedMain.o b/obj/fastaFromBedMain.o
index 05a7de8ad70b4f099534838f6e7258508d66a55c..fee4bea8373cba27b238e07ad47490354a812f83 100644
Binary files a/obj/fastaFromBedMain.o and b/obj/fastaFromBedMain.o differ
diff --git a/obj/genomeCoverageMain.o b/obj/genomeCoverageMain.o
index b67dc2fd9c3745dfb64078c3f615859e7bc7e16e..65e7f22fbb878c2b636225d338decfb72874eaba 100644
Binary files a/obj/genomeCoverageMain.o and b/obj/genomeCoverageMain.o differ
diff --git a/obj/intersectMain.o b/obj/intersectMain.o
index 9cca477298576c31fedfdc7f83b212d65847e1b4..b35dad0d5236ecb98a1eefbb9688124d2d0db607 100644
Binary files a/obj/intersectMain.o and b/obj/intersectMain.o differ
diff --git a/obj/linksBed.o b/obj/linksBed.o
index b079e718af4016933873e96781f240db63cecde9..1eedf49df47149bfc8d12de03fc5282c5c32346d 100644
Binary files a/obj/linksBed.o and b/obj/linksBed.o differ
diff --git a/obj/linksMain.o b/obj/linksMain.o
index b7633c87ba7629b1085837e1d6039e7418a73939..9c5d449b9a34262ce59dca483170c2793633f61f 100644
Binary files a/obj/linksMain.o and b/obj/linksMain.o differ
diff --git a/obj/maskFastaFromBedMain.o b/obj/maskFastaFromBedMain.o
index 6a5cc9288dae0ab76c07590fc6db9e9726634a4a..385e3971b6f459081cf85a5b1b1f8b74d1d4b1da 100644
Binary files a/obj/maskFastaFromBedMain.o and b/obj/maskFastaFromBedMain.o differ
diff --git a/obj/mergeMain.o b/obj/mergeMain.o
index a96d80a88d54d52936c15a4fc0563fb6315f2b96..ba6917072c8cc0c552dfcfac17c896454235abdf 100644
Binary files a/obj/mergeMain.o and b/obj/mergeMain.o differ
diff --git a/obj/shuffleBed.o b/obj/shuffleBed.o
index f4d2e246b979023d911e56de2f37aaf603d99d66..e2daa269ef4b9f4bd84f0e08dcf92236ec127d55 100644
Binary files a/obj/shuffleBed.o and b/obj/shuffleBed.o differ
diff --git a/obj/shuffleBedMain.o b/obj/shuffleBedMain.o
index 751a91bee16048f27ad47daf42896c6c022cb3ee..21b657d239336dfec3112380f4dcca31b6b53a3d 100644
Binary files a/obj/shuffleBedMain.o and b/obj/shuffleBedMain.o differ
diff --git a/obj/slopBed.o b/obj/slopBed.o
index db9fe4c7886ad811de30e93a833ca216b0c51c12..4a2c31ef9acdf8fb3613f58c32f388c851a375fe 100644
Binary files a/obj/slopBed.o and b/obj/slopBed.o differ
diff --git a/obj/slopBedMain.o b/obj/slopBedMain.o
index b3737678d073eb8418a23cd2b213c180e8a49fbf..4e69135d6db193c514aed80f991696074531e13a 100644
Binary files a/obj/slopBedMain.o and b/obj/slopBedMain.o differ
diff --git a/obj/sortBed.o b/obj/sortBed.o
index 3510300236f06484f64c4a5113b3f65592187b5b..387fbda237a7fb80ba8776c03bb3b86b475299fe 100644
Binary files a/obj/sortBed.o and b/obj/sortBed.o differ
diff --git a/obj/sortMain.o b/obj/sortMain.o
index 237c870bc132b6ba89f9b1ef02e3b8a3b6cb6777..aa38a8b5f46e8f94b752af06f59b65d41b478ce9 100644
Binary files a/obj/sortMain.o and b/obj/sortMain.o differ
diff --git a/obj/subtractMain.o b/obj/subtractMain.o
index bac1071bb7757279587c2a347f95a9c0b3fccb71..6d96a2d4d69cd354b7b0a19694ec73c2b029eb6d 100644
Binary files a/obj/subtractMain.o and b/obj/subtractMain.o differ
diff --git a/obj/windowMain.o b/obj/windowMain.o
index a2503d02d43ca837fdc79e3f376607a1d0125194..f170f6166eda2ca3cac4ac3aae49aafa5bada8ca 100644
Binary files a/obj/windowMain.o and b/obj/windowMain.o differ
diff --git a/src/closestBed/closestMain.cpp b/src/closestBed/closestMain.cpp
index 19ad244fc56bf7bc86588b4e42d996c876011771..e3f5da62b96ac4fdc8b4758e53634bf2e5ae9346 100755
--- a/src/closestBed/closestMain.cpp
+++ b/src/closestBed/closestMain.cpp
@@ -102,21 +102,21 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cerr << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+ cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
- cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+ cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
- cerr << "SUMMARY: For each feature in BED A, finds the closest " << endl;
- cerr << "\t feature (upstream or downstream) in BED B." << endl << endl;
+ cerr << "Summary: For each feature in BED A, finds the closest " << endl;
+ cerr << "\t\t feature (upstream or downstream) in BED B." << endl << endl;
- cerr << "USAGE: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
- cerr << "OPTIONS: " << endl;
- cerr << "\t-s\t" << "Force strandedness. That is, find the closest feature in B" << endl;
+ cerr << "Options: " << endl;
+ cerr << "\t-s\t" << "Force strandedness. That is, find the closest feature in B" << endl;
cerr << "\t\tthat overlaps A on the same strand." << endl;
cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
- cerr << "\t-t\t" << "How ties for closest feature are handled. This occurs when two" << endl;
+ cerr << "\t-t\t" << "How ties for closest feature are handled. This occurs when two" << endl;
cerr << "\t\tfeatures in B have exactly the same overlap with A." << endl;
cerr << "\t\tBy default, all such features in B are reported." << endl;
cerr << "\t\tHere are all the options:" << endl;
@@ -125,7 +125,7 @@ void ShowHelp(void) {
cerr << "\t\t- \"last\" Report the last tie that occurred in the B file." << endl << endl;
- cerr << "NOTES: " << endl;
+ cerr << "Notes: " << endl;
cerr << "\tReports \"none\" for chrom and \"-1\" for all other fields when a feature" << endl;
cerr << "\tis not found in B on the same chromosome as the feature in A." << endl;
cerr << "\tE.g. none\t-1\t-1" << endl << endl;
diff --git a/src/coverageBed/coverageMain.cpp b/src/coverageBed/coverageMain.cpp
index 954db15abc7684f5909cef7ebbe7ba94f7c6ba75..7fb04ef2b886ac1768960a573f4135342366c278 100755
--- a/src/coverageBed/coverageMain.cpp
+++ b/src/coverageBed/coverageMain.cpp
@@ -94,16 +94,16 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cerr << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+ cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
- cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+ cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
- cerr << "SUMMARY: Returns the depth and breadth of coverage of features from A" << endl;
- cerr << "\t on the intervals in B." << endl << endl;
+ cerr << "Summary: Returns the depth and breadth of coverage of features from A" << endl;
+ cerr << "\t\t on the intervals in B." << endl << endl;
- cerr << "USAGE: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
- cerr << "OUTPUT: " << endl;
+ cerr << "Output: " << endl;
cerr << "\t" << " After each entry in B, reports: " << endl;
cerr << "\t 1) The number of features in A that overlapped the B interval." << endl;
cerr << "\t 2) The number of bases in B that had non-zero coverage." << endl;
diff --git a/src/fastaFromBed/fastaFromBedMain.cpp b/src/fastaFromBed/fastaFromBedMain.cpp
index 9806fd86be383382e3d95c1ce5e11cab9706d113..72c4a0673ee6a7299bdd419646edf27149169a4f 100755
--- a/src/fastaFromBed/fastaFromBedMain.cpp
+++ b/src/fastaFromBed/fastaFromBedMain.cpp
@@ -103,19 +103,19 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cerr << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+ cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
- cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+ cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
- cerr << "SUMMARY: Extract DNA sequences into a fasta file based on BED coordinates." << endl << endl;
+ cerr << "Summary: Extract DNA sequences into a fasta file based on BED coordinates." << endl << endl;
- cerr << "USAGE: " << PROGRAM_NAME << " [OPTIONS] -fi -bed -fo " << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -fi -bed -fo " << endl << endl;
- cerr << "OPTIONS: " << endl;
- cerr << "\t\t-fi\tInput FASTA file" << endl;
- cerr << "\t\t-bed\tBED file of ranges to extract from -fi" << endl;
- cerr << "\t\t-fo\tOutput FASTA file" << endl;
- cerr << "\t\t-name\tUse the BED name field (#4) for the FASTA header" << endl;
+ cerr << "Options: " << endl;
+ cerr << "\t-fi\t\tInput FASTA file" << endl;
+ cerr << "\t-bed\tBED file of ranges to extract from -fi" << endl;
+ cerr << "\t-fo\t\tOutput FASTA file" << endl;
+ cerr << "\t-name\tUse the BED name field (#4) for the FASTA header" << endl;
diff --git a/src/genomeCoverageBed/genomeCoverageMain.cpp b/src/genomeCoverageBed/genomeCoverageMain.cpp
index edfbb63e7c392e4667c8102ac636d02e71b79886..ec05802ae222aa0125692fe42af3938de81a5da4 100755
--- a/src/genomeCoverageBed/genomeCoverageMain.cpp
+++ b/src/genomeCoverageBed/genomeCoverageMain.cpp
@@ -105,23 +105,23 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cerr << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+ cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
- cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+ cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
- cerr << "SUMMARY: Compute the coverage of a BED (-i) file on genome (-g) file." << endl << endl;
+ cerr << "Summary: Compute the coverage of a BED file among a genome." << endl << endl;
- cerr << "USAGE: " << PROGRAM_NAME << " [OPTIONS] -g <genome> -i <bed>" << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -g <genome> -i <bed>" << endl << endl;
- cerr << "OPTIONS: " << endl;
- cerr << "\t-d\t" << "Report the depth at each genome position." << endl;
- cerr << "\t\tDefault behavior is to report a histogram." << endl << endl;
+ cerr << "Options: " << endl;
+ cerr << "\t-d\t\t" << "Report the depth at each genome position." << endl;
+ cerr << "\t\t\tDefault behavior is to report a histogram." << endl << endl;
cerr << "\t-max\t" << "Combine all positions with a depth >= max into" << endl;
- cerr << "\t\ta single bin in the histogram." << endl;
- cerr << "\t\t- (INTEGER)" << endl << endl;
+ cerr << "\t\t\ta single bin in the histogram." << endl;
+ cerr << "\t\t\t- (INTEGER)" << endl << endl;
- cerr << "NOTES: " << endl;
+ cerr << "Notes: " << endl;
cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl;
cerr << "\t <chromName><TAB><chromSize>" << endl << endl;
cerr << "\tFor example, Human (hg19):" << endl;
@@ -134,7 +134,7 @@ void ShowHelp(void) {
cerr << "\t A simple \"sort -k 1,1 <BED> > <BED>.sorted\" will suffice."<< endl << endl;
- cerr << "TIPS: " << endl;
+ cerr << "Tips: " << endl;
cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl;
cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl;
cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e /" << endl;
diff --git a/src/intersectBed/genes.gff b/src/intersectBed/genes.gff
index 4d8883e5f69022f5d9753ef47cc1aee9e24fb2bb..9415e80d61d04ed5541d0eff21b9a6537634f37b 100644
--- a/src/intersectBed/genes.gff
+++ b/src/intersectBed/genes.gff
@@ -1459,4 +1459,3 @@ chr1 hg19_knownGene exon 1238542 1238661 0.000000 - . gene_id "uc001aeb.2"; tran
chr1 hg19_knownGene CDS 1239466 1239523 0.000000 - 1 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
chr1 hg19_knownGene exon 1239466 1239523 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
chr1 hg19_knownGene CDS 1243149 1243195 0.000000 - 0 gene_id "uc001aeb.2"; transcrip
-
diff --git a/src/intersectBed/intersectMain.cpp b/src/intersectBed/intersectMain.cpp
index b2b7de957dfb81325e84fa8de27051582e1ba537..6adaaaa6fb67e73cb0bbcf610c0dd8b7b9a7e894 100755
--- a/src/intersectBed/intersectMain.cpp
+++ b/src/intersectBed/intersectMain.cpp
@@ -151,15 +151,15 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cerr << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+ cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
- cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+ cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
- cerr << "SUMMARY: Report overlaps between a.bed and b.bed." << endl << endl;
+ cerr << "Summary: Report overlaps between a.bed and b.bed." << endl << endl;
- cerr << "USAGE: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
- cerr << "OPTIONS: " << endl;
+ cerr << "Options: " << endl;
cerr << "\t-wa\t" << "Write the original entry in A for each overlap." << endl << endl;
cerr << "\t-wb\t" << "Write the original entry in B for each overlap." << endl;
cerr << "\t\t- Useful for knowing _what_ A overlaps. Restricted by -f." << endl << endl;
diff --git a/src/linksBed/a.bed b/src/linksBed/a.bed
new file mode 100644
index 0000000000000000000000000000000000000000..c7f1f6fe149868ee3e61cf8554114c5ff138aee8
--- /dev/null
+++ b/src/linksBed/a.bed
@@ -0,0 +1 @@
+chr1 0 12000 a 1 +
diff --git a/src/linksBed/genes.bed b/src/linksBed/genes.bed
new file mode 100644
index 0000000000000000000000000000000000000000..ab05940b47db89efb5ad309ba47a12b3a3a158fd
--- /dev/null
+++ b/src/linksBed/genes.bed
@@ -0,0 +1,829 @@
+chr21 9928613 10012791 uc002yip.1 0 -
+chr21 9928613 10012791 uc002yiq.1 0 -
+chr21 9928613 10012791 uc002yir.1 0 -
+chr21 9928613 10012791 uc010gkv.1 0 -
+chr21 9928613 10061300 uc002yis.1 0 -
+chr21 10042683 10120796 uc002yit.1 0 -
+chr21 10042683 10120808 uc002yiu.1 0 -
+chr21 10079666 10120808 uc002yiv.1 0 -
+chr21 10080031 10081687 uc002yiw.1 0 -
+chr21 10081660 10120796 uc002yix.2 0 -
+chr21 13332351 13346202 uc002yiy.2 0 +
+chr21 13336975 13346202 uc002yiz.2 0 +
+chr21 13361138 13412440 uc002yja.2 0 +
+chr21 13904368 13935777 uc002yjb.1 0 +
+chr21 13944438 13944477 uc002yjc.1 0 +
+chr21 13945076 13945106 uc002yjd.1 0 +
+chr21 13973491 13975330 uc002yje.1 0 -
+chr21 14137333 14142556 uc002yjf.1 0 -
+chr21 14200023 14200052 uc002yjg.1 0 +
+chr21 14202070 14202096 uc002yjh.1 0 -
+chr21 14237966 14274631 uc002yji.1 0 -
+chr21 14270940 14274631 uc002yjj.2 0 -
+chr21 14321612 14438647 uc002yjk.2 0 +
+chr21 14321612 14438730 uc002yjl.2 0 +
+chr21 14403005 14501125 uc002yjm.1 0 -
+chr21 14459414 14483611 uc010gkw.1 0 -
+chr21 14510336 14522564 uc002yjo.2 0 +
+chr21 14510336 14522564 uc002yjn.2 0 +
+chr21 14510336 14522564 uc002yjp.2 0 +
+chr21 14567990 14585577 uc002yjq.1 0 +
+chr21 14567990 14595563 uc002yjr.1 0 +
+chr21 14567990 14595563 uc010gkx.1 0 +
+chr21 14567990 14632206 uc002yjs.2 0 +
+chr21 14665307 14677380 uc002yjt.1 0 -
+chr21 14779419 14840535 uc002yju.1 0 -
+chr21 14779419 14840535 uc010gky.1 0 -
+chr21 14779419 14877594 uc002yjv.1 0 -
+chr21 15117160 15151900 uc002yjw.1 0 -
+chr21 15255426 15262718 uc002yjx.1 0 -
+chr21 15258731 15358997 uc010gkz.1 0 -
+chr21 16024366 16174248 uc002yjy.1 0 +
+chr21 16024366 16174248 uc002yjz.1 0 +
+chr21 16024366 16174248 uc010gla.1 0 +
+chr21 16085691 16113036 uc010glb.1 0 +
+chr21 16364712 16901413 uc002ykb.1 0 +
+chr21 16364712 16901413 uc002yka.1 0 +
+chr21 16365304 16365529 uc010glc.1 0 +
+chr21 16488569 16901413 uc002ykc.1 0 +
+chr21 16833279 16833360 uc002ykd.1 0 +
+chr21 16834014 16834106 uc002yke.1 0 +
+chr21 16884427 16884516 uc002ykf.1 0 +
+chr21 17733107 17743132 uc002ykg.1 0 +
+chr21 17807200 17859800 uc002ykh.1 0 +
+chr21 17807200 17859800 uc010gld.1 0 +
+chr21 17807200 17859800 uc010gle.1 0 +
+chr21 17807200 17861137 uc002yki.1 0 +
+chr21 17841215 17887768 uc002ykj.1 0 +
+chr21 17887841 17907033 uc002ykk.1 0 -
+chr21 17887841 17907033 uc002ykl.1 0 -
+chr21 18071593 18086697 uc002ykm.2 0 -
+chr21 18071593 18086697 uc002ykn.2 0 -
+chr21 18083154 18113574 uc002ykq.2 0 -
+chr21 18083154 18113574 uc002yko.2 0 -
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diff --git a/src/linksBed/genes.gff b/src/linksBed/genes.gff
new file mode 100644
index 0000000000000000000000000000000000000000..9415e80d61d04ed5541d0eff21b9a6537634f37b
--- /dev/null
+++ b/src/linksBed/genes.gff
@@ -0,0 +1,1461 @@
+chr1 hg19_knownGene exon 11874 12227 0.000000 + . gene_id "uc001aaa.3"; transcript_id "uc001aaa.3";
+chr1 hg19_knownGene exon 12613 12721 0.000000 + . gene_id "uc001aaa.3"; transcript_id "uc001aaa.3";
+chr1 hg19_knownGene exon 13221 14409 0.000000 + . gene_id "uc001aaa.3"; transcript_id "uc001aaa.3";
+chr1 hg19_knownGene start_codon 12190 12192 0.000000 + . gene_id "uc010nxq.1"; transcript_id "uc010nxq.1";
+chr1 hg19_knownGene CDS 12190 12227 0.000000 + 0 gene_id "uc010nxq.1"; transcript_id "uc010nxq.1";
+chr1 hg19_knownGene exon 11874 12227 0.000000 + . gene_id "uc010nxq.1"; transcript_id "uc010nxq.1";
+chr1 hg19_knownGene CDS 12595 12721 0.000000 + 1 gene_id "uc010nxq.1"; transcript_id "uc010nxq.1";
+chr1 hg19_knownGene exon 12595 12721 0.000000 + . gene_id "uc010nxq.1"; transcript_id "uc010nxq.1";
+chr1 hg19_knownGene CDS 13403 13639 0.000000 + 0 gene_id "uc010nxq.1"; transcript_id "uc010nxq.1";
+chr1 hg19_knownGene exon 13403 14409 0.000000 + . gene_id "uc010nxq.1"; transcript_id "uc010nxq.1";
+chr1 hg19_knownGene exon 11874 12227 0.000000 + . gene_id "uc010nxr.1"; transcript_id "uc010nxr.1";
+chr1 hg19_knownGene exon 12646 12697 0.000000 + . gene_id "uc010nxr.1"; transcript_id "uc010nxr.1";
+chr1 hg19_knownGene exon 13221 14409 0.000000 + . gene_id "uc010nxr.1"; transcript_id "uc010nxr.1";
+chr1 hg19_knownGene exon 14363 14829 0.000000 - . gene_id "uc009vis.2"; transcript_id "uc009vis.2";
+chr1 hg19_knownGene exon 14970 15038 0.000000 - . gene_id "uc009vis.2"; transcript_id "uc009vis.2";
+chr1 hg19_knownGene exon 15796 15942 0.000000 - . gene_id "uc009vis.2"; transcript_id "uc009vis.2";
+chr1 hg19_knownGene exon 16607 16765 0.000000 - . gene_id "uc009vis.2"; transcript_id "uc009vis.2";
+chr1 hg19_knownGene exon 14363 14829 0.000000 - . gene_id "uc009vit.2"; transcript_id "uc009vit.2";
+chr1 hg19_knownGene exon 14970 15038 0.000000 - . gene_id "uc009vit.2"; transcript_id "uc009vit.2";
+chr1 hg19_knownGene exon 15796 15947 0.000000 - . gene_id "uc009vit.2"; transcript_id "uc009vit.2";
+chr1 hg19_knownGene exon 16607 16765 0.000000 - . gene_id "uc009vit.2"; transcript_id "uc009vit.2";
+chr1 hg19_knownGene exon 16858 17055 0.000000 - . gene_id "uc009vit.2"; transcript_id "uc009vit.2";
+chr1 hg19_knownGene exon 17233 17742 0.000000 - . gene_id "uc009vit.2"; transcript_id "uc009vit.2";
+chr1 hg19_knownGene exon 17915 18061 0.000000 - . gene_id "uc009vit.2"; transcript_id "uc009vit.2";
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diff --git a/src/linksBed/genes.html b/src/linksBed/genes.html
new file mode 100644
index 0000000000000000000000000000000000000000..3469d5fca06908ec41df7b46f89e8a74717e8fd7
--- /dev/null
+++ b/src/linksBed/genes.html
@@ -0,0 +1,11603 @@
+<html>
+ <body>
+<title>genes.bed</title>
+<br>Firefox users: Press and hold the "apple" or "alt" key and click link to open in new tab.
+<p style="font-family:courier">
+<table border="0" align="justify"
+<h3>BED Entries from: stdin </h3>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:9928613-10012791>chr21:9928613-10012791</a>
+ </td>
+ <td>
+uc002yip.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:9928613-10012791>chr21:9928613-10012791</a>
+ </td>
+ <td>
+uc002yiq.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:9928613-10012791>chr21:9928613-10012791</a>
+ </td>
+ <td>
+uc002yir.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:9928613-10012791>chr21:9928613-10012791</a>
+ </td>
+ <td>
+uc010gkv.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
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+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46381326-46399909>chr21:46381326-46399909</a>
+ </td>
+ <td>
+uc010gqg.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46405497-46428729>chr21:46405497-46428729</a>
+ </td>
+ <td>
+uc002zii.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46432787-46473119>chr21:46432787-46473119</a>
+ </td>
+ <td>
+uc002zij.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46433466-46473079>chr21:46433466-46473079</a>
+ </td>
+ <td>
+uc002zik.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46433466-46473119>chr21:46433466-46473119</a>
+ </td>
+ <td>
+uc002zil.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46473585-46496032>chr21:46473585-46496032</a>
+ </td>
+ <td>
+uc002zim.2
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46473585-46496032>chr21:46473585-46496032</a>
+ </td>
+ <td>
+uc002zin.2
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46479475-46491502>chr21:46479475-46491502</a>
+ </td>
+ <td>
+uc002zio.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46479475-46503607>chr21:46479475-46503607</a>
+ </td>
+ <td>
+uc002zip.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46479475-46511294>chr21:46479475-46511294</a>
+ </td>
+ <td>
+uc002ziq.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46479475-46529664>chr21:46479475-46529664</a>
+ </td>
+ <td>
+uc002zir.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46480565-46496171>chr21:46480565-46496171</a>
+ </td>
+ <td>
+uc002zis.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46530694-46536539>chr21:46530694-46536539</a>
+ </td>
+ <td>
+uc002zit.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46530694-46536539>chr21:46530694-46536539</a>
+ </td>
+ <td>
+uc002ziu.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46530694-46542093>chr21:46530694-46542093</a>
+ </td>
+ <td>
+uc002ziv.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46530694-46542093>chr21:46530694-46542093</a>
+ </td>
+ <td>
+uc002ziw.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46530694-46542093>chr21:46530694-46542093</a>
+ </td>
+ <td>
+uc002zix.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46530694-46542093>chr21:46530694-46542093</a>
+ </td>
+ <td>
+uc002ziy.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46530694-46542093>chr21:46530694-46542093</a>
+ </td>
+ <td>
+uc010gqh.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46537349-46539139>chr21:46537349-46539139</a>
+ </td>
+ <td>
+uc010gqi.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46544772-46562562>chr21:46544772-46562562</a>
+ </td>
+ <td>
+uc002ziz.2
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46544772-46565167>chr21:46544772-46565167</a>
+ </td>
+ <td>
+uc002zja.2
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46545474-46563479>chr21:46545474-46563479</a>
+ </td>
+ <td>
+uc002zjc.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46545474-46568213>chr21:46545474-46568213</a>
+ </td>
+ <td>
+uc002zjf.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46545477-46568213>chr21:46545477-46568213</a>
+ </td>
+ <td>
+uc010gqj.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46559057-46568213>chr21:46559057-46568213</a>
+ </td>
+ <td>
+uc002zjg.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46568463-46690110>chr21:46568463-46690110</a>
+ </td>
+ <td>
+uc002zji.2
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46569229-46690110>chr21:46569229-46690110</a>
+ </td>
+ <td>
+uc002zjj.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46578738-46594162>chr21:46578738-46594162</a>
+ </td>
+ <td>
+uc010gqk.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46699327-46703021>chr21:46699327-46703021</a>
+ </td>
+ <td>
+uc002zjk.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46703317-46790647>chr21:46703317-46790647</a>
+ </td>
+ <td>
+uc002zjl.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46703317-46791548>chr21:46703317-46791548</a>
+ </td>
+ <td>
+uc002zjm.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46703317-46791548>chr21:46703317-46791548</a>
+ </td>
+ <td>
+uc010gql.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46703317-46794451>chr21:46703317-46794451</a>
+ </td>
+ <td>
+uc002zjn.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46703317-46813028>chr21:46703317-46813028</a>
+ </td>
+ <td>
+uc002zjo.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46748653-46789614>chr21:46748653-46789614</a>
+ </td>
+ <td>
+uc002zjp.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46783075-46791548>chr21:46783075-46791548</a>
+ </td>
+ <td>
+uc002zjq.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46797251-46803437>chr21:46797251-46803437</a>
+ </td>
+ <td>
+uc002zjr.2
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46805625-46813028>chr21:46805625-46813028</a>
+ </td>
+ <td>
+uc002zjs.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46808123-46813028>chr21:46808123-46813028</a>
+ </td>
+ <td>
+uc002zjt.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46842958-46849463>chr21:46842958-46849463</a>
+ </td>
+ <td>
+uc002zju.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46842958-46849463>chr21:46842958-46849463</a>
+ </td>
+ <td>
+uc002zjv.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46879954-46904483>chr21:46879954-46904483</a>
+ </td>
+ <td>
+uc002zjw.2
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46879954-46909291>chr21:46879954-46909291</a>
+ </td>
+ <td>
+uc002zjx.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46879954-46909291>chr21:46879954-46909291</a>
+ </td>
+ <td>
+uc002zjy.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46879954-46909291>chr21:46879954-46909291</a>
+ </td>
+ <td>
+uc010gqm.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr21:46887625-46906276>chr21:46887625-46906276</a>
+ </td>
+ <td>
+uc002zjz.1
+ </td>
+ <td>
+0
+ </td>
+ <td>
++
+ </td>
+</tr>
+</table>
+</p>
+ </body>
+</html>
diff --git a/src/linksBed/linksBed.cpp b/src/linksBed/linksBed.cpp
index 96f0bb16fb8833bb374eb54d0ea569d4a724f87a..3736b080fd2ce3f564a53c561884788aeff89a20 100755
--- a/src/linksBed/linksBed.cpp
+++ b/src/linksBed/linksBed.cpp
@@ -1,12 +1,14 @@
-//
-// linksBed.cpp
-// BEDTools
-//
-// Created by Aaron Quinlan Spring 2009.
-// Copyright 2009 Aaron Quinlan. All rights reserved.
-//
-// Summary: Creates HTML or UCSC browser coordinates from a BED file.
-//
+/*****************************************************************************
+ linksBed.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
#include "lineFileUtilities.h"
#include "linksBed.h"
@@ -57,7 +59,7 @@ void BedLinks::WriteURL(BED &bed, string &base) {
cout << bed.score << endl;
cout << "\t</td>" << endl;
}
- else if (this->bed->bedType == 6) {
+ else if ((this->bed->bedType == 6) || (this->bed->bedType == 9) || (this->bed->bedType == 12)) {
cout << "\t<td>" << endl;
cout << bed.name << endl;
cout << "\t</td>" << endl;
@@ -74,7 +76,7 @@ void BedLinks::WriteURL(BED &bed, string &base) {
}
-void BedLinks::LinksBed() {
+void BedLinks::LinksBed(istream &bedInput) {
// construct the html base.
@@ -96,72 +98,42 @@ void BedLinks::LinksBed() {
cout << "<p style=\"font-family:courier\">" << endl;
cout << "<table border=\"0\" align=\"justify\"" << endl;
+ string bedLine;
+ BED bedEntry;
+ int lineNum = 0;
+ vector<string> bedFields;
+ bedFields.reserve(12);
- // Are we dealing with a BED file or a BED passed via stdin?
+ cout << "<h3>BED Entries from: stdin </h3>" << endl;
- // Case 1: Proper BED File.
- if ( (this->bedFile != "") && (this->bedFile != "stdin") ) {
+ while (getline(bedInput, bedLine)) {
- // open the BED file for reading
- ifstream bed(bedFile.c_str(), ios::in);
- if ( !bed ) {
- cerr << "Error: The requested bed file (" <<bedFile << ") could not be opened. Exiting!" << endl;
- exit (1);
+ Tokenize(bedLine,bedFields);
+ lineNum++;
+
+ if (this->bed->parseLine(bedEntry, bedFields, lineNum)) {
+ bedEntry.count = 0;
+ WriteURL(bedEntry, base);
}
+ bedFields.clear();
+ }
+ cout << "</table>" << endl;
+ cout << "</p>" << endl;
+ cout << "\t</body>" << endl <<"</html>" << endl;
+}
- string bedLine;
- BED bedEntry;
- int lineNum = 0;
-
- cout << "<h3>BED Entries from: " << this->bedFile << "</h3>" << endl;
-
- while (getline(bed, bedLine)) {
- if ((bedLine.find("track") != string::npos) || (bedLine.find("browser") != string::npos)) {
- continue;
- }
- else {
- vector<string> bedFields;
- Tokenize(bedLine,bedFields);
+void BedLinks::DetermineBedInput() {
- lineNum++;
-
- if (this->bed->parseBedLine(bedEntry, bedFields, lineNum)) {
- bedEntry.count = 0;
- WriteURL(bedEntry, base);
- }
- }
+ if (this->bedFile != "stdin") { // process a file
+ ifstream beds(this->bedFile.c_str(), ios::in);
+ if ( !beds ) {
+ cerr << "Error: The requested bed file (" << this->bedFile << ") could not be opened. Exiting!" << endl;
+ exit (1);
}
- cout << "</table>" << endl;
- cout << "</p>" << endl;
- cout << "\t</body>" << endl <<"</html>" << endl;
+ LinksBed(beds);
}
- // Case 2: STDIN.
- else {
- string bedLine;
- BED bedEntry;
- int lineNum = 0;
-
- cout << "<h3>BED Entries from: stdin </h3>" << endl;
-
- while (getline(cin, bedLine)) {
-
- if ((bedLine.find("track") != string::npos) || (bedLine.find("browser") != string::npos)) {
- continue;
- }
- else {
- vector<string> bedFields;
- Tokenize(bedLine,bedFields);
-
- lineNum++;
- if (this->bed->parseBedLine(bedEntry, bedFields, lineNum)) {
- bedEntry.count = 0;
- WriteURL(bedEntry, base);
- }
- }
- }
- cout << "</table>" << endl;
- cout << "</p>" << endl;
- cout << "\t</body>" << endl <<"</html>" << endl;
+ else { // process stdin
+ LinksBed(cin);
}
}
diff --git a/src/linksBed/linksBed.h b/src/linksBed/linksBed.h
index a5ff327b5b117a5076241c2b54ddf57ee28d9787..06e8b8510c056954744020b0a8ac0349d4ca2cfb 100755
--- a/src/linksBed/linksBed.h
+++ b/src/linksBed/linksBed.h
@@ -1,3 +1,14 @@
+/*****************************************************************************
+ linksBed.h
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
#include "bedFile.h"
#include <vector>
#include <algorithm>
@@ -20,8 +31,9 @@ public:
~BedLinks(void);
void WriteURL(BED &, string &);
- void LinksBed(); // the default. sorts by chrom (asc.) then by start (asc.)
-
+ void LinksBed(istream &bedInput); // the default. sorts by chrom (asc.) then by start (asc.)
+ void DetermineBedInput();
+
private:
string bedFile;
string base;
diff --git a/src/linksBed/linksMain.cpp b/src/linksBed/linksMain.cpp
index bd742683cf517ab4f651553b0b9f568bd2f486c5..3b244344b4bbf933bb373171f04f96fb0cdd094c 100755
--- a/src/linksBed/linksMain.cpp
+++ b/src/linksBed/linksMain.cpp
@@ -1,3 +1,14 @@
+/*****************************************************************************
+ linksBedMain.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
#include "linksBed.h"
#include "version.h"
@@ -21,18 +32,14 @@ int main(int argc, char* argv[]) {
// input files
string bedFile;
bool haveBed = false;
-
- /* Defaults for Quinlan
- //string org = "mouse";
- //string db = "mm9";
- //string base = "http://mirror.bioch.virginia.edu";
- */
/* Defaults for everyone else */
string org = "human";
string db = "hg18";
string base = "http://genome.ucsc.edu";
+ if(argc <= 1) showHelp = true;
+
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
@@ -80,7 +87,7 @@ int main(int argc, char* argv[]) {
if (!showHelp) {
BedLinks *bl = new BedLinks(bedFile, base, org, db);
- bl->LinksBed();
+ bl->DetermineBedInput();
return 0;
}
else {
@@ -90,31 +97,28 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cerr << "===============================================" << endl;
- cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
- cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com) " << endl ;
- cerr << " Hall Laboratory, University of Virginia" << endl;
- cerr << "===============================================" << endl << endl;
- cerr << "Description: Creates HTML links from a BED file." << endl << endl;
- cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed> > out.html" << endl << endl;
-
- cerr << "OPTIONS: " << endl;
- cerr << "\t" << "-base\t\t" << "The browser basename. Default: http://genome.ucsc.edu " << endl << endl;
- cerr << "\t" << "-org\t\t" << "The organism. Default: human" << endl << endl;
- cerr << "\t" << "-db\t\t" << "The build. Default: hg18" << endl << endl;
-
- cerr << "NOTES: " << endl;
- cerr << "\t" << "-i stdin\t" << "Allows BED file to be read from stdin. E.g.: cat a.bed | linksBed -i stdin > out.html" << endl << endl;
- cerr << "\t***Only tab-delimited BED3 - BED6 formats allowed.***"<< endl << endl;
+ cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
- cerr << "EXAMPLE: " << endl;
- cerr << "\t" << "By default, the links created will point to the human (hg18) UCSC browser. If you have a local mirror, you can override this behavior";
- cerr << "by supplying the -base, -org, and -db options." << endl;
- cerr << "\t" << "For example, if the main URL of your local mirror for mouse MM9 is called: http://mymirror.myuniversity.edu, then you would use the following parameters:" << endl;
- cerr << "\t\t" << "-base http://mymirror.myuniversity.edu" << endl;
- cerr << "\t\t" << "-org mouse" << endl;
- cerr << "\t\t" << "-db mm9" << endl;
- // end the program here
- exit(1);
+ cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
+
+ cerr << "Summary: Creates HTML links to an UCSC Genome Browser from a BED file." << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed> > out.html" << endl << endl;
+
+ cerr << "Options: " << endl;
+ cerr << "\t-base\t" << "The browser basename. Default: http://genome.ucsc.edu " << endl;
+ cerr << "\t-org\t" << "The organism. Default: human" << endl;
+ cerr << "\t-db\t\t" << "The build. Default: hg18" << endl << endl;
+
+ cerr << "Example: " << endl;
+ cerr << "\t" << "By default, the links created will point to the human (hg18) UCSC browser." << endl;
+ cerr << "\tIf you have a local mirror, you can override this behavior by supplying" << endl;
+ cerr << "\tthe -base, -org, and -db options." << endl << endl;
+ cerr << "\t" << "For example, if the main URL of your local mirror for mouse MM9 is called: " << endl;
+ cerr << "\thttp://mymirror.myuniversity.edu, then you would use the following:" << endl;
+ cerr << "\t" << "-base http://mymirror.myuniversity.edu" << endl;
+ cerr << "\t" << "-org mouse" << endl;
+ cerr << "\t" << "-db mm9" << endl;
+
+ exit(1);
}
diff --git a/src/linksBed/test.html b/src/linksBed/test.html
new file mode 100644
index 0000000000000000000000000000000000000000..e793cdd5f7daca0b7a3087ac1806ca04f575517d
--- /dev/null
+++ b/src/linksBed/test.html
@@ -0,0 +1,20465 @@
+<html>
+ <body>
+<title>stdin</title>
+<br>Firefox users: Press and hold the "apple" or "alt" key and click link to open in new tab.
+<p style="font-family:courier">
+<table border="0" align="justify"
+<h3>BED Entries from: stdin </h3>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:11873-12227>chr1:11873-12227</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:12612-12721>chr1:12612-12721</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:13220-14409>chr1:13220-14409</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:12189-12192>chr1:12189-12192</a>
+ </td>
+ <td>
+start_codon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:12189-12227>chr1:12189-12227</a>
+ </td>
+ <td>
+CDS
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:11873-12227>chr1:11873-12227</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:12594-12721>chr1:12594-12721</a>
+ </td>
+ <td>
+CDS
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:12594-12721>chr1:12594-12721</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:13402-13639>chr1:13402-13639</a>
+ </td>
+ <td>
+CDS
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:13402-14409>chr1:13402-14409</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:11873-12227>chr1:11873-12227</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:12645-12697>chr1:12645-12697</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:13220-14409>chr1:13220-14409</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
++
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:14362-14829>chr1:14362-14829</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:14969-15038>chr1:14969-15038</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:15795-15942>chr1:15795-15942</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:16606-16765>chr1:16606-16765</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:14362-14829>chr1:14362-14829</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:14969-15038>chr1:14969-15038</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:15795-15947>chr1:15795-15947</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:16606-16765>chr1:16606-16765</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:16857-17055>chr1:16857-17055</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:17232-17742>chr1:17232-17742</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:17914-18061>chr1:17914-18061</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:18267-18366>chr1:18267-18366</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:18912-19759>chr1:18912-19759</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:14362-14829>chr1:14362-14829</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:14969-15038>chr1:14969-15038</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:15795-15947>chr1:15795-15947</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:16606-16765>chr1:16606-16765</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:16857-17055>chr1:16857-17055</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:17232-17368>chr1:17232-17368</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:17605-17742>chr1:17605-17742</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:17914-18061>chr1:17914-18061</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:18267-18366>chr1:18267-18366</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:18912-19759>chr1:18912-19759</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:14362-14829>chr1:14362-14829</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:14969-15038>chr1:14969-15038</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:15795-15947>chr1:15795-15947</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:16606-16765>chr1:16606-16765</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:16857-17055>chr1:16857-17055</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:17232-17742>chr1:17232-17742</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:17914-18061>chr1:17914-18061</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:18267-18369>chr1:18267-18369</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:18500-18554>chr1:18500-18554</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:18912-19759>chr1:18912-19759</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:14362-14829>chr1:14362-14829</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
+0.000000
+ </td>
+ <td>
+-
+ </td>
+</tr>
+<tr>
+ <td>
+ <a href=http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&position=chr1:14969-15038>chr1:14969-15038</a>
+ </td>
+ <td>
+exon
+ </td>
+ <td>
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+</html>
diff --git a/src/maskFastaFromBed/maskFastaFromBedMain.cpp b/src/maskFastaFromBed/maskFastaFromBedMain.cpp
index 5c0b17b7c14a9c966b91c2df38cf60777b30f580..8002f3d7d0b0d4707c92fcd141367174a57c23a0 100755
--- a/src/maskFastaFromBed/maskFastaFromBedMain.cpp
+++ b/src/maskFastaFromBed/maskFastaFromBedMain.cpp
@@ -105,19 +105,19 @@ void ShowHelp(void) {
- cerr << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+ cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
- cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+ cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
- cerr << "SUMMARY: Mask a fasta file based on BED coordinates." << endl << endl;
+ cerr << "Summary: Mask a fasta file based on BED coordinates." << endl << endl;
- cerr << "USAGE: " << PROGRAM_NAME << " [OPTIONS] -fi -out -bed" << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -fi -out -bed" << endl << endl;
- cerr << "OPTIONS:" << endl;
- cerr << "\t\t-fi\tInput FASTA file" << endl;
- cerr << "\t\t-bed\tBED file of ranges to mask in -fi" << endl;
- cerr << "\t\t-fo\tOutput FASTA file" << endl;
- cerr << "\t\t-soft\tEnforce \"soft\" masking. That is, instead of masking with Ns," << endl;
+ cerr << "Options:" << endl;
+ cerr << "\t-fi\t\tInput FASTA file" << endl;
+ cerr << "\t-bed\tBED file of ranges to mask in -fi" << endl;
+ cerr << "\t-fo\t\tOutput FASTA file" << endl;
+ cerr << "\t-soft\tEnforce \"soft\" masking. That is, instead of masking with Ns," << endl;
cerr << "\t\t\tmask with lower-case bases." << endl;
// end the program here
diff --git a/src/mergeBed/mergeMain.cpp b/src/mergeBed/mergeMain.cpp
index bd4038bd864cb8f79ed643cdc1bcadaf8e139b9d..f00037ea646cdf7f78d77e5a82ef6d78a7927938 100755
--- a/src/mergeBed/mergeMain.cpp
+++ b/src/mergeBed/mergeMain.cpp
@@ -108,15 +108,15 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cerr << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+ cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
- cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+ cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
- cerr << "SUMMARY: Merges overlapping BED entries into a single interval." << endl << endl;
+ cerr << "Summary: Merges overlapping BED entries into a single interval." << endl << endl;
- cerr << "USAGE: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
- cerr << "OPTIONS: " << endl;
+ 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\t- By default, merging is done without respect to strand." << endl << endl;
diff --git a/src/shuffleBed/a.bed b/src/shuffleBed/a.bed
new file mode 100644
index 0000000000000000000000000000000000000000..147fcc3f4cba11b785baf64491de65895d523f61
--- /dev/null
+++ b/src/shuffleBed/a.bed
@@ -0,0 +1,2 @@
+chr1 0 100 a1 1 +
+chr1 0 1000 a2 2 -
diff --git a/src/shuffleBed/exclude.bed b/src/shuffleBed/exclude.bed
new file mode 100644
index 0000000000000000000000000000000000000000..c03d074e62de06c9d5fe062c77f91a805bd361ea
--- /dev/null
+++ b/src/shuffleBed/exclude.bed
@@ -0,0 +1 @@
+chr1 0 100
diff --git a/src/shuffleBed/exlude b/src/shuffleBed/exlude
new file mode 100644
index 0000000000000000000000000000000000000000..ebf5a92e1126f64c65ba2ac93ac5810091befd3d
--- /dev/null
+++ b/src/shuffleBed/exlude
@@ -0,0 +1 @@
+chr1 100 1000
diff --git a/src/shuffleBed/genome b/src/shuffleBed/genome
new file mode 100644
index 0000000000000000000000000000000000000000..63286768ec0f8cb9a34c4c2802a9be1e2f87ed7f
--- /dev/null
+++ b/src/shuffleBed/genome
@@ -0,0 +1 @@
+chr1 10000
diff --git a/src/shuffleBed/shuffleBed.cpp b/src/shuffleBed/shuffleBed.cpp
index f339cdca89e325f3d2616d36d96d23ec76ea3d14..ebedbef462c184a03b527273596a434aaebc410b 100755
--- a/src/shuffleBed/shuffleBed.cpp
+++ b/src/shuffleBed/shuffleBed.cpp
@@ -1,11 +1,14 @@
-//
-// shuffleBed.cpp
-// BEDTools
-//
-// Created by Aaron Quinlan Spring 2009.
-// Copyright 2009 Aaron Quinlan. All rights reserved.
-//
-//
+/*****************************************************************************
+ shuffleBed.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
#include "lineFileUtilities.h"
#include "shuffleBed.h"
@@ -51,7 +54,7 @@ BedShuffle::~BedShuffle(void) {
-void BedShuffle::Shuffle() {
+void BedShuffle::Shuffle(istream &bedInput) {
// open the GENOME file for reading.
@@ -75,37 +78,32 @@ void BedShuffle::Shuffle() {
}
}
- // open the input BED file for reading.
- // if successful, store the start and end positions
- // for each entry (per chromosome)
- ifstream beds(this->bedFile.c_str(), ios::in);
- if ( !beds ) {
- cerr << "Error: The requested bed file (" <<this->bedFile << ") could not be opened. Exiting!" << endl;
- exit (1);
- }
-
+
BED bedEntry; // used to store the current BED line from the BED file.
int lineNum = 0;
string bedLine; // used to store the current (unparsed) line from the BED file.
+ vector<string> bedFields;
+ bedFields.reserve(12);
+
+ while (getline(bedInput, bedLine)) {
- while (getline(beds, bedLine)) {
-
- vector<string> bedFields;
+
Tokenize(bedLine,bedFields);
lineNum++;
+
+ if (bed->parseLine(bedEntry, bedFields, lineNum)) {
- if (this->bed->parseBedLine(bedEntry, bedFields, lineNum)) {
-
// choose a new locus for this feat
ChooseLocus(bedEntry);
bed->reportBedNewLine(bedEntry);
}
+ bedFields.clear();
}
}
-void BedShuffle::ShuffleWithExclusions() {
+void BedShuffle::ShuffleWithExclusions(istream &bedInput) {
// open the GENOME file for reading.
@@ -129,38 +127,28 @@ void BedShuffle::ShuffleWithExclusions() {
}
}
- // open the input BED file for reading.
- // if successful, store the start and end positions
- // for each entry (per chromosome)
- ifstream beds(this->bedFile.c_str(), ios::in);
- if ( !beds ) {
- cerr << "Error: The requested bed file (" <<this->bedFile << ") could not be opened. Exiting!" << endl;
- exit (1);
- }
-
BED bedEntry; // used to store the current BED line from the BED file.
int lineNum = 0;
string bedLine; // used to store the current (unparsed) line from the BED file.
-
-
- while (getline(beds, bedLine)) {
+ vector<string> bedFields;
+ bedFields.reserve(12);
+ vector<BED> hits;
+ hits.reserve(100);
+
+ while (getline(bedInput, bedLine)) {
- vector<string> bedFields;
Tokenize(bedLine,bedFields);
lineNum++;
- if (this->bed->parseBedLine(bedEntry, bedFields, lineNum)) {
+ if (bed->parseLine(bedEntry, bedFields, lineNum)) {
// choose a random locus
ChooseLocus(bedEntry);
- /*
- test to see if the chosen locus overlaps
- with an exclude region
- */
- vector<BED> hits;
- exclude->binKeeperFind(exclude->bedMap[bedEntry.chrom], bedEntry.start, bedEntry.end, hits);
-
+ // test to see if the chosen locus overlaps
+ // with an exclude region
+ exclude->binKeeperFind(exclude->bedMap[bedEntry.chrom], bedEntry.start, bedEntry.end, hits);
+
bool haveOverlap = false;
for (vector<BED>::const_iterator h = hits.begin(); h != hits.end(); ++h) {
@@ -208,6 +196,7 @@ void BedShuffle::ShuffleWithExclusions() {
bed->reportBedNewLine(bedEntry);
}
}
+ bedFields.clear();
}
}
@@ -264,3 +253,21 @@ void BedShuffle::ChooseLocus(BED &bedEntry) {
}
}
+
+void BedShuffle::DetermineBedInput() {
+ if (bed->bedFile != "stdin") { // process a file
+ ifstream beds(bed->bedFile.c_str(), ios::in);
+ if ( !beds ) {
+ cerr << "Error: The requested bed file (" << bed->bedFile << ") could not be opened. Exiting!" << endl;
+ exit (1);
+ }
+ if (this->haveExclude) { ShuffleWithExclusions(beds); }
+ else {Shuffle(beds); }
+ }
+ else {
+ // process stdin
+ if (this->haveExclude) { ShuffleWithExclusions(cin); }
+ else {Shuffle(cin); }
+ }
+}
+
diff --git a/src/shuffleBed/shuffleBed.h b/src/shuffleBed/shuffleBed.h
index e8654adaec20eafdd1b1769f000a7178bf03eeb0..900315e5ac48668731fc56f39dcb5c1a32aae852 100755
--- a/src/shuffleBed/shuffleBed.h
+++ b/src/shuffleBed/shuffleBed.h
@@ -1,3 +1,14 @@
+/*****************************************************************************
+ shuffleBed.h
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
#include "bedFile.h"
#include <vector>
#include <iostream>
@@ -17,16 +28,18 @@ class BedShuffle {
public:
-// constructor
+ // constructor
BedShuffle(string &, string &, string &, bool &, bool &, bool &, int &);
-// destructor
+ // destructor
~BedShuffle(void);
- void Shuffle();
- void ShuffleWithExclusions();
+ void Shuffle(istream &bedInput);
+ void ShuffleWithExclusions(istream &bedInput);
void ChooseLocus(BED &);
+
+ void DetermineBedInput();
private:
diff --git a/src/shuffleBed/shuffleBedMain.cpp b/src/shuffleBed/shuffleBedMain.cpp
index 74eb5e9783db884d7092ea3381d9ae8b1393b0ca..004a19cb6d432de91f890edba9aa4c167d7bcad7 100755
--- a/src/shuffleBed/shuffleBedMain.cpp
+++ b/src/shuffleBed/shuffleBedMain.cpp
@@ -1,3 +1,14 @@
+/*****************************************************************************
+ shuffleBedMain.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
#include "shuffleBed.h"
#include "version.h"
@@ -59,17 +70,17 @@ int main(int argc, char* argv[]) {
genomeFile = argv[i + 1];
i++;
}
- else if(PARAMETER_CHECK("-x", 2, parameterLength)) {
+ else if(PARAMETER_CHECK("-excl", 5, parameterLength)) {
haveExclude = true;
excludeFile = argv[i + 1];
i++;
}
- else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
+ else if(PARAMETER_CHECK("-seed", 5, parameterLength)) {
haveSeed = true;
seed = atoi(argv[i + 1]);
i++;
}
- else if(PARAMETER_CHECK("-sameChrom", 10, parameterLength)) {
+ else if(PARAMETER_CHECK("-chrom", 6, parameterLength)) {
sameChrom = true;
}
else {
@@ -87,13 +98,8 @@ int main(int argc, char* argv[]) {
if (!showHelp) {
BedShuffle *bc = new BedShuffle(bedFile, genomeFile, excludeFile, haveSeed, haveExclude, sameChrom, seed);
- if (haveExclude) {
- bc->ShuffleWithExclusions();
- }
- else {
- bc->Shuffle();
- }
-
+ bc->DetermineBedInput();
+
return 0;
}
else {
@@ -103,33 +109,41 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cerr << "===============================================" << endl;
- cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
- cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com) " << endl ;
- cerr << " Hall Laboratory, University of Virginia" << endl;
- cerr << "===============================================" << endl << endl;
- cerr << "Description: Randomly shuffle the locations of a BED (-i) file among a genome (-g)." << endl << endl;
- cerr << "***NOTE: Only tab-delimited BED3 - BED6 formats allowed.***"<< endl;
-
- cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -g <genome> -i <bed>" << endl << endl;
+ cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
+
+ cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
- cerr << "OPTIONS: " << endl;
- cerr << "\t" << "-x\t\t\t" << "A BED file of coordinates in which features in -i should not be placed (e.g. gaps.bed)." << endl;
- cerr << "\t" << "-sameChrom\t\t" << "Keep features in -i on the same chromosome. By default, the chrom and position are randomly chosen." << endl << endl;
- cerr << "\t" << "-s\t\t\t" << "Supply an integer seed for the shuffling. By default, the seed is chosen automatically." << endl << endl;
-
-
- cerr << "NOTES: " << endl;
- cerr << "\tThe genome file should tab delimited and structured as follows: <chr><TAB><size>. For example, Mus musculus:" << endl;
- cerr << "\t\tchr1\t197195432" << endl;
- cerr << "\t\tchr2\t181748087" << endl;
- cerr << "\t\t..." << endl;
- cerr << "\t\tchrY_random\t58682461" << endl << endl;
+ cerr << "Summary: Randomly permute the locations of a BED file among a genome." << endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -g <genome> -i <bed>" << endl << endl;
+
+ cerr << "Options: " << endl;
+ cerr << "\t-excl\t" << "A BED file of coordinates in which features in -i" << endl;
+ cerr << "\t\t\tshould not be placed (e.g. gaps.bed)." << endl << endl;
+
+ cerr << "\t-chrom\t" << "Keep features in -i on the same chromosome."<< endl;
+ cerr << "\t\t\t- By default, the chrom and position are randomly chosen." << endl << endl;
+
+ cerr << "\t-seed\t" << "Supply an integer seed for the shuffling." << endl;
+ cerr << "\t\t\t- By default, the seed is chosen automatically." << endl;
+ cerr << "\t\t\t- (INTEGER)" << endl << endl;
+
+
+ cerr << "Notes: " << endl;
+ cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl;
+ cerr << "\t <chromName><TAB><chromSize>" << endl << endl;
+ cerr << "\tFor example, Human (hg19):" << endl;
+ cerr << "\tchr1\t249250621" << endl;
+ cerr << "\tchr2\t243199373" << endl;
+ cerr << "\t..." << endl;
+ cerr << "\tchr18_gl000207_random\t4262" << endl << endl;
+
- cerr << "TIPS:" << endl;
- cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract chromosome sizes. For example, H. sapiens:" << endl << endl;
- cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \"select chrom, size from hg18.chromInfo\" > hg18.genome"
- << endl << endl;
+ cerr << "Tips: " << endl;
+ cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl;
+ cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl;
+ cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e /" << endl;
+ cerr << "\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" << endl << endl;
// end the program here
diff --git a/src/shuffleBed/test b/src/shuffleBed/test
new file mode 100644
index 0000000000000000000000000000000000000000..286859e5960da47f2bc82cb13a7015f3be2c9415
--- /dev/null
+++ b/src/shuffleBed/test
@@ -0,0 +1 @@
+chr1 0 100 a1 1 +
diff --git a/src/slopBed/a.bed b/src/slopBed/a.bed
new file mode 100644
index 0000000000000000000000000000000000000000..318e7de9da7666bd01d5757f02c1982a06be4c74
--- /dev/null
+++ b/src/slopBed/a.bed
@@ -0,0 +1,3 @@
+chr1 100 200 a1 1 +
+chr1 100 200 a2 2 -
+
diff --git a/src/slopBed/genome b/src/slopBed/genome
new file mode 100644
index 0000000000000000000000000000000000000000..0dd8b222927c0b6b0c0ca8bd85b2e420fd8ea121
--- /dev/null
+++ b/src/slopBed/genome
@@ -0,0 +1 @@
+chr1 1000
diff --git a/src/slopBed/slopBed.cpp b/src/slopBed/slopBed.cpp
index 316b4059ae0aa2f0b1cb984267141ddd1332dc1c..2e748bc47c38058a724c07c4466f29e8e4438928 100755
--- a/src/slopBed/slopBed.cpp
+++ b/src/slopBed/slopBed.cpp
@@ -1,10 +1,14 @@
-/*
- BEDTools: slopBed.cpp
-
- Created by Aaron Quinlan Spring 2009.
- Copyright 2009 Aaron Quinlan. All rights reserved.
-*/
+/*****************************************************************************
+ slopBed.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+ Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
#include "lineFileUtilities.h"
#include "slopBed.h"
@@ -33,44 +37,6 @@ BedSlop::~BedSlop(void) {
}
-
-void BedSlop::DetermineBedInput() {
-
-
- /* open the GENOME file for reading.
- if successful, load each chrom and it's size into
- the "chromSize" map. also compute the total size of the genome
- and store in "genomeSize"
- */
- ifstream genome(this->genomeFile.c_str(), ios::in);
- if ( !genome ) {
- cerr << "Error: The requested genome file (" <<this->genomeFile << ") could not be opened. Exiting!" << endl;
- exit (1);
- }
- else {
- string chrom;
- unsigned int size;
- while (genome >> chrom >> size) {
- if (chrom.size() > 0 && size > 0) {
- this->chromSizes[chrom] = size;
- }
- }
- }
-
- if (this->bedFile != "stdin") { // process a file
- ifstream beds(this->bedFile.c_str(), ios::in);
- if ( !beds ) {
- cerr << "Error: The requested bed file (" << this->bedFile << ") could not be opened. Exiting!" << endl;
- exit (1);
- }
- ProcessBed(beds);
- }
- else { // process stdin
- ProcessBed(cin);
- }
-}
-
-
void BedSlop::SlopBed(istream &bedInput) {
BED bedEntry; // used to store the current BED line from the BED file.
@@ -87,7 +53,7 @@ void BedSlop::SlopBed(istream &bedInput) {
if a valid BED entry, add requested "slop" and print out
the adjusted BED entry.
*/
- if (this->bed->parseBedLine(bedEntry, bedFields, lineNum)) {
+ if (this->bed->parseLine(bedEntry, bedFields, lineNum)) {
AddSlop(bedEntry);
bed->reportBedNewLine(bedEntry);
}
@@ -95,7 +61,6 @@ void BedSlop::SlopBed(istream &bedInput) {
}
-
void BedSlop::AddSlop(BED &bed) {
/*
@@ -123,3 +88,38 @@ void BedSlop::AddSlop(BED &bed) {
}
+void BedSlop::DetermineBedInput() {
+
+
+ /* open the GENOME file for reading.
+ if successful, load each chrom and it's size into
+ the "chromSize" map. also compute the total size of the genome
+ and store in "genomeSize"
+ */
+ ifstream genome(this->genomeFile.c_str(), ios::in);
+ if ( !genome ) {
+ cerr << "Error: The requested genome file (" <<this->genomeFile << ") could not be opened. Exiting!" << endl;
+ exit (1);
+ }
+ else {
+ string chrom;
+ unsigned int size;
+ while (genome >> chrom >> size) {
+ if (chrom.size() > 0 && size > 0) {
+ this->chromSizes[chrom] = size;
+ }
+ }
+ }
+
+ if (this->bedFile != "stdin") { // process a file
+ ifstream beds(this->bedFile.c_str(), ios::in);
+ if ( !beds ) {
+ cerr << "Error: The requested bed file (" << this->bedFile << ") could not be opened. Exiting!" << endl;
+ exit (1);
+ }
+ SlopBed(beds);
+ }
+ else { // process stdin
+ SlopBed(cin);
+ }
+}
diff --git a/src/slopBed/slopBed.h b/src/slopBed/slopBed.h
index bcdf31075fd1cde9a9a3b86e19c50be3d64b9d2c..272ca7976bbc1fb7554ffd7e9ac5dfb32f299d98 100755
--- a/src/slopBed/slopBed.h
+++ b/src/slopBed/slopBed.h
@@ -4,8 +4,18 @@
#include <fstream>
#include <map>
#include <cstdlib>
-#include <ctime>
+/*****************************************************************************
+ slopBed.h
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+ Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
+#include <ctime>
using namespace std;
@@ -22,13 +32,13 @@ public:
// destructor
~BedSlop(void);
- void DetermineBedInput();
-
void SlopBed(istream &bedInput);
// method to add requested "slop" to a single BED entry
void AddSlop(BED &bed);
+ void DetermineBedInput();
+
private:
string bedFile;
diff --git a/src/slopBed/slopBedMain.cpp b/src/slopBed/slopBedMain.cpp
index 5bb22e386b6a9401f8d4e2a7376a903dd9b3c0ec..4d162372e8657a1daa9ad558afad5d72bb3905fa 100755
--- a/src/slopBed/slopBedMain.cpp
+++ b/src/slopBed/slopBedMain.cpp
@@ -1,3 +1,14 @@
+/*****************************************************************************
+ slopBedMain.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
#include "slopBed.h"
#include "version.h"
@@ -104,6 +115,7 @@ int main(int argc, char* argv[]) {
cerr << endl << "*****" << endl << "*****ERROR: Must supply -l and -r with -s. " << endl << "*****" << endl;
showHelp = true;
}
+
if (!showHelp) {
BedSlop *bc = new BedSlop(bedFile, genomeFile, forceStrand, leftSlop, rightSlop);
bc->DetermineBedInput();
@@ -117,36 +129,47 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cerr << "===============================================" << endl;
- cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
- cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com) " << endl ;
- cerr << " Hall Laboratory, University of Virginia" << endl;
- cerr << "===============================================" << endl << endl;
- cerr << "Description: Add requested base pairs of \"slop\" to each BED entry." << endl << endl;
-
- cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -g <genome> -i <bed>" << endl << endl;
+ cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
+
+ cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
+
+ cerr << "Summary: Add requested base pairs of \"slop\" to each BED entry." << endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed> -g <genome> [-b <int> or (-l and -r)]" << endl << endl;
+
+ cerr << "Options: " << endl;
+ cerr << "\t-b\t" << "Increase the BED entry by the same number base pairs in each direction." << endl;
+ cerr << "\t\t- (Integer)" << endl;
+
+ cerr << "\t-l\t" << "The number of base pairs to subtract from the start coordinate." << endl;
+ cerr << "\t\t- (Integer)" << endl;
+
+ cerr << "\t-r\t" << "The number of base pairs to add to the end coordinate." << endl;
+ cerr << "\t\t- (Integer)" << endl;
+
+ cerr << "\t-s\t" << "Define -l and -r based on strand." << endl;
+ cerr << "\t\tE.g. if used, -l 500 for a negative-stranded feature, " << endl;
+ cerr << "\t\tit will add 500 bp downstream. Default = false." << endl << endl;
+
+ cerr << "Notes: " << endl;
+ cerr << "\t(1) Starts will be set to 0 if the requested slop would force it below 0." << endl;
+ cerr << "\t(2) Ends will be set to the chromosome length if the requested slop would" << endl;
+ cerr << "\t\t force it above the max chrom length." << endl;
+
+ cerr << "\t(3) The genome file should tab delimited and structured as follows:" << endl;
+ cerr << "\t <chromName><TAB><chromSize>" << endl << endl;
+ cerr << "\tFor example, Human (hg19):" << endl;
+ cerr << "\tchr1\t249250621" << endl;
+ cerr << "\tchr2\t243199373" << endl;
+ cerr << "\t..." << endl;
+ cerr << "\tchr18_gl000207_random\t4262" << endl << endl;
+
- cerr << "OPTIONS: " << endl;
- cerr << "\t" << "-l\t\t\t" << "The number of base pairs to subtract from the start coordinate." << endl;
- cerr << "\t" << "-r\t\t\t" << "The number of base pairs to add to the end coordinate." << endl;
- cerr << "\t" << "-b\t\t\t" << "Increase the BED entry by the same number base pairs in each direction." << endl;
- cerr << "\t" << "-s\t\t\t" << "Define -l and -r based on strand. E.g. if used, -l 500 for a negative-stranded " << endl << "\t\t\t\tfeature, it will add 500 bp downstream. Default = false." << endl << endl;
-
- cerr << "NOTES: " << endl;
- cerr << "\t1. Starts will be corrected to 0 if the requested slop would force it below 0." << endl;
- cerr << "\t2. Ends will be corrected to the chromosome length if the requested slop would force it above the max chrom length." << endl;
- cerr << "\t3. The genome file should tab delimited and structured as follows: <chr><TAB><size>. For example, Mus musculus:" << endl;
- cerr << "\t\tchr1\t197195432" << endl;
- cerr << "\t\tchr2\t181748087" << endl;
- cerr << "\t\t..." << endl;
- cerr << "\t\tchrY_random\t58682461" << endl;
- cerr << "\t4. -i stdin\t" << "Allows BED file to be read from stdin. E.g.: cat a.bed | slopBed -i stdin" << endl;
- cerr << "\t5. ***Only tab-delimited BED3 - BED6 formats allowed.***"<< endl << endl;
-
- cerr << "TIPS:" << endl;
- cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract chromosome sizes. For example, H. sapiens:" << endl << endl;
- cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \"select chrom, size from hg18.chromInfo\" > hg18.genome"
- << endl << endl;
+ cerr << "Tips: " << endl;
+ cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl;
+ cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl;
+ cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e /" << endl;
+ cerr << "\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" << endl << endl;
// end the program here
diff --git a/src/sortBed/a.bed b/src/sortBed/a.bed
new file mode 100644
index 0000000000000000000000000000000000000000..cb7131d75a1d1836f82be03e0cdd5aaeea6496ad
--- /dev/null
+++ b/src/sortBed/a.bed
@@ -0,0 +1,5 @@
+chr1 800 1000
+chr1 80 180
+chr1 1 10
+chr1 750 10000
+
diff --git a/src/sortBed/sortBed.cpp b/src/sortBed/sortBed.cpp
index 235a7f7255000341fc0e216d24213dccaf8e9d99..f61b322dc536c5b8ee626c6f20fb8c44bf5e1386 100755
--- a/src/sortBed/sortBed.cpp
+++ b/src/sortBed/sortBed.cpp
@@ -1,12 +1,14 @@
-//
-// sortBed.cpp
-// BEDTools
-//
-// Created by Aaron Quinlan Spring 2009.
-// Copyright 2009 Aaron Quinlan. All rights reserved.
-//
-// Summary: Sorts a BED file in ascending order by chrom then by start position.
-//
+/*****************************************************************************
+ sortBed.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
#include "lineFileUtilities.h"
#include "sortBed.h"
diff --git a/src/sortBed/sortBed.h b/src/sortBed/sortBed.h
index 60c6067cfa3ae52ffec723729af5f00a45cf98de..48125995bec0c5e971bcd8c1266d1da7c2cf2b87 100755
--- a/src/sortBed/sortBed.h
+++ b/src/sortBed/sortBed.h
@@ -1,3 +1,14 @@
+/*****************************************************************************
+ sortBed.h
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
#include "bedFile.h"
#include <vector>
#include <algorithm>
diff --git a/src/sortBed/sortMain.cpp b/src/sortBed/sortMain.cpp
index 45436d116bb6f6b998d9d27db9a12cfa3d59c806..bfb83edbdbf6f8629f688722b9674a81d3878f13 100755
--- a/src/sortBed/sortMain.cpp
+++ b/src/sortBed/sortMain.cpp
@@ -1,3 +1,14 @@
+/*****************************************************************************
+ sortBedMain.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
#include "sortBed.h"
#include "version.h"
@@ -30,6 +41,8 @@ int main(int argc, char* argv[]) {
bool sortByChromThenScoreAsc = false;
bool sortByChromThenScoreDesc = false;
+ if(argc <= 1) showHelp = true;
+
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
@@ -131,26 +144,20 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cerr << "===============================================" << endl;
- cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
- cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com) " << endl ;
- cerr << " Hall Laboratory, University of Virginia" << endl;
- cerr << "===============================================" << endl << endl;
- cerr << "Description: Sorts a BED file in various and useful ways." << endl << endl;
- cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
-
- cerr << "OPTIONS: " << endl;
- cerr << "\t" << "-sizeA\t\t" << "Sort the BED file by feature size in ascending order. Sorts across all chromosomes." << endl << endl;
- cerr << "\t" << "-sizeD\t\t" << "Sort the BED file by feature size in descending order. Sorts across all chromosomes." << endl << endl;
- cerr << "\t" << "-chrThenSizeA\t" << "Sort the BED file by chrom (ascending), then feature size in ascending order." << endl << endl;
- cerr << "\t" << "-chrThenSizeD\t" << "Sort the BED file by chrom (ascending), then feature size in descending order." << endl << endl;
- cerr << "\t" << "-chrThenScoreA\t" << "Sort the BED file by chrom (ascending), then score in ascending order." << endl << endl;
- cerr << "\t" << "-chrThenScoreD\t" << "Sort the BED file by chrom (ascending), then scor size in descending order." << endl << endl;
+ cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
+
+ cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
+ cerr << "Summary: Sorts a BED file in various and useful ways." << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
+
+ cerr << "Options: " << endl;
+ cerr << "\t" << "-sizeA\t\t" << "Sort by feature size in ascending order." << endl;
+ cerr << "\t" << "-sizeD\t\t" << "Sort by feature size in descending order." << endl;
+ cerr << "\t" << "-chrThenSizeA\t" << "Sort by chrom (asc), then feature size (asc)." << endl;
+ cerr << "\t" << "-chrThenSizeD\t" << "Sort by chrom (asc), then feature size (desc)." << endl;
+ cerr << "\t" << "-chrThenScoreA\t" << "Sort by chrom (asc), then score (asc)." << endl;
+ cerr << "\t" << "-chrThenScoreD\t" << "Sort by chrom (asc), then score (desc)." << endl << endl;
- cerr << "NOTES: " << endl;
- cerr << "\t" << "-i stdin\t\t" << "Allows BED file A to be read from stdin. E.g.: cat a.bed | sortBed -i stdin" << endl << endl;
- cerr << "\t***Only tab-delimited BED3 - BED6 formats allowed.***"<< endl << endl;
- // end the program here
exit(1);
}
diff --git a/src/subtractBed/subtractMain.cpp b/src/subtractBed/subtractMain.cpp
index d503d3f0dd5d5d9decf64630b6c94bc2bf5c5bcf..eccbc736b7f5ee6ff01e1eb0b43a085767ae65b9 100755
--- a/src/subtractBed/subtractMain.cpp
+++ b/src/subtractBed/subtractMain.cpp
@@ -107,16 +107,16 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cerr << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+ cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
- cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+ cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
- cerr << "SUMMARY: Removes the portion(s) of an interval that is overlapped" << endl;
- cerr << "\t by another feature(s)." << endl << endl;
+ cerr << "Summary: Removes the portion(s) of an interval that is overlapped" << endl;
+ cerr << "\t\t by another feature(s)." << endl << endl;
- cerr << "USAGE: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
- cerr << "OPTIONS: " << endl;
+ cerr << "Options: " << endl;
cerr << "\t-f\t" << "Minimum overlap required as a fraction of A." << endl;
cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
cerr << "\t\t- (FLOAT) (e.g. 0.50)" << endl << endl;
diff --git a/src/windowBed/windowMain.cpp b/src/windowBed/windowMain.cpp
index f6d2e20dbbb257f693ed3bae5ddafb6fc887960d..dbe92896623841918014036725e85de43dc3837e 100755
--- a/src/windowBed/windowMain.cpp
+++ b/src/windowBed/windowMain.cpp
@@ -162,17 +162,17 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cerr << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+ cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
- cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+ cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
- cerr << "SUMMARY: Examines a \"window\" around each feature in A and" << endl;
- cerr << "\t reports all features in B that overlap the window. For each" << endl;
- cerr << "\t overlap the entire entry in A and B are reported." << endl << endl;
+ cerr << "Summary: Examines a \"window\" around each feature in A and" << endl;
+ cerr << "\t\t reports all features in B that overlap the window. For each" << endl;
+ cerr << "\t\t overlap the entire entry in A and B are reported." << endl << endl;
- cerr << "USAGE: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
- cerr << "OPTIONS: " << endl;
+ cerr << "Options: " << endl;
cerr << "\t-w\t" << "Base pairs added upstream and downstream of each entry" << endl;
cerr << "\t\tin A when searching for overlaps in B." << endl;
cerr << "\t\t- Creates symterical \"windows\" around A." << endl;