From 939d5390d94154f792b3c1edb167f7fb1005cdd0 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Mon, 16 Aug 2010 16:51:16 -0400
Subject: [PATCH] Cleaned up groupBy and unionBedFiles.
---
Makefile | 1 +
src/groupBy/groupBy.cpp | 29 ++++++++++++-------------
src/utils/bedFile/bedFile.cpp | 41 -----------------------------------
3 files changed, 15 insertions(+), 56 deletions(-)
diff --git a/Makefile b/Makefile
index 6cb24583..363fbd1b 100644
--- a/Makefile
+++ b/Makefile
@@ -37,6 +37,7 @@ SUBDIRS = $(SRC_DIR)/bamToBed \
UTIL_SUBDIRS = $(SRC_DIR)/utils/lineFileUtilities \
$(SRC_DIR)/utils/bedFile \
+ $(SRC_DIR)/utils/bedGraphFile \
$(SRC_DIR)/utils/tabFile \
$(SRC_DIR)/utils/genomeFile \
$(SRC_DIR)/utils/gzstream \
diff --git a/src/groupBy/groupBy.cpp b/src/groupBy/groupBy.cpp
index 000e0687..6396af95 100644
--- a/src/groupBy/groupBy.cpp
+++ b/src/groupBy/groupBy.cpp
@@ -185,27 +185,26 @@ void ShowHelp(void) {
cerr << "\t-grp\t" << "Specify the columns (1-based) for the grouping." << endl;
cerr << "\t\tThe columns must be comma separated." << endl;
- cerr << "\t\tDefault: 1,2,3" << endl << endl;
+ cerr << "\t\t- Default: 1,2,3" << endl << endl;
- cerr << "\t-opCol\t" << "Specify the column (1-based) that should be summarized." << endl;
- cerr << "\t\tRequired." << endl << endl;
+ cerr << "\t-opCols\t" << "Specify the column (1-based) that should be summarized." << endl;
+ cerr << "\t\t- Required." << endl << endl;
- cerr << "\t-op\t" << "Specify the operation that should be applied to opCol." << endl;
+ cerr << "\t-ops\t" << "Specify the operation that should be applied to opCol." << endl;
cerr << "\t\tValid operations: sum, count, min, max, mean, median," << endl;
- cerr << "\t\tmode, antimode, stdev, collapse (i.e., print a comma separated list)" << endl;
- cerr << "\t\tDefault: sum" << endl;
+ cerr << "\t\tmode, antimode, stdev, sstdev (sample standard dev.), and" << endl;
+ cerr << "\t\tcollapse (i.e., print a comma separated list)" << endl;
+ cerr << "\t\t- Default: sum" << endl << endl;
cerr << "Examples: " << endl;
- cerr << "\t$ cat test.out" << endl;
- cerr << "\tchr1 10 20 A chr1 15 25 1000" << endl;
- cerr << "\tchr1 10 20 A chr1 25 35 10000" << endl << endl;
- cerr << "\t$ cat test.out | groupBy -i stdin -grp 1,2,3,4 -opCol 8 -op sum" << endl;
+ cerr << "\t$ cat ex1.out" << endl;
+ cerr << "\tchr1 10 20 A chr1 15 25 B.1 1000" << endl;
+ cerr << "\tchr1 10 20 A chr1 25 35 B.2 10000" << endl << endl;
+ cerr << "\t$ groupBy -i ex1.out -grp 1,2,3,4 -opCols 9 -ops sum" << endl;
cerr << "\tchr1 10 20 A 11000" << endl << endl;
- cerr << "\t$ cat test.out | groupBy -i stdin -grp 1,2,3,4 -opCol 8 -op max" << endl;
- cerr << "\tchr1 10 20 A 1000" << endl << endl;
- cerr << "\t$ cat test.out | groupBy -i stdin -grp 1,2,3,4 -opCol 8 -op mean" << endl;
- cerr << "\tchr1 10 20 A 5500" << endl << endl;
- cerr << "\t$ cat test.out | groupBy -i stdin -grp 1,2,3,4 -opCol 8 -op collapse" << endl;
+ cerr << "\t$ groupBy -i ex1.out -grp 1,2,3,4 -opCols 9,9 -ops sum,max" << endl;
+ cerr << "\tchr1 10 20 A 11000 10000" << endl << endl;
+ cerr << "\t$ groupBy -i ex1.out -grp 1,2,3,4 -opCols 8,9 -ops collapse,mean" << endl;
cerr << "\tchr1 10 20 A 1000,10000," << endl << endl;
cerr << "Notes: " << endl;
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index ab612c90..7610a15a 100644
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -163,47 +163,6 @@ void BedFile::Open(void) {
cerr << "Error: Unexpected file type (" << bedFile << "). Exiting!" << endl;
exit(1);
}
-
- // Old method.
- /*
- else {
- size_t foundPos;
- foundPos = bedFile.find_last_of(".gz");
- // is this a GZIPPED BED file?
- if (foundPos == bedFile.size() - 1) {
- igzstream beds(bedFile.c_str(), ios::in);
- if ( !beds ) {
- cerr << "Error: The requested bed file (" << bedFile << ") could not be opened. Exiting!" << endl;
- exit (1);
- }
- else {
- // if so, close it (this was just a test)
- beds.close();
- // now set a pointer to the stream so that we
- // can read the file later on.
- // Thank God for Josuttis, p. 631!
- _bedStream = new igzstream(bedFile.c_str(), ios::in);
- }
- }
- // not GZIPPED.
- else {
-
- ifstream beds(bedFile.c_str(), ios::in);
- // can we open the file?
- if ( !beds ) {
- cerr << "Error: The requested bed file (" << bedFile << ") could not be opened. Exiting!" << endl;
- exit (1);
- }
- else {
- // if so, close it (this was just a test)
- beds.close();
- // now set a pointer to the stream so that we
- // can read the file later on.
- // Thank God for Josuttis, p. 631!
- _bedStream = new ifstream(bedFile.c_str(), ios::in);
- }
- }
- }*/
}
--
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