From fb5efebf3ec402740e2ef93edcc04f7bd63232e7 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Mon, 4 Jan 2010 14:12:08 -0500
Subject: [PATCH] Further standardization of the option listings.
---
bin/closestBed | Bin 90224 -> 90224 bytes
bin/pairToPair | Bin 113728 -> 113728 bytes
bin/subtractBed | Bin 90080 -> 90080 bytes
bin/windowBed | Bin 94216 -> 94216 bytes
obj/closestMain.o | Bin 8680 -> 8680 bytes
obj/pairToPairMain.o | Bin 8884 -> 8884 bytes
obj/subtractMain.o | Bin 7136 -> 7136 bytes
obj/windowMain.o | Bin 12360 -> 12360 bytes
src/closestBed/closestMain.cpp | 2 +-
src/pairToPair/pairToPairMain.cpp | 2 +-
src/subtractBed/subtractMain.cpp | 2 +-
src/windowBed/windowMain.cpp | 4 ++--
12 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/bin/closestBed b/bin/closestBed
index d7851134769e85b0bc9950affad51cf5e8e11e2b..e94cc484f592158187dd08fabfa9014021dbfc07 100755
GIT binary patch
delta 53
zcmV-50LuUHzy<KY1+ZWS5Pa|*rG=~%_jy|P&JUQS__J^Z{sRFllWz(t0RXd_3fIAt
La?Ccfr_9NdxO*Ah
delta 53
zcmV-50LuUHzy<KY1+ZWS5F#2={!Tyw(1lhAIwm(RTeENm{sRFmlWz(t0Rgj`3fIAt
LaLhNesLaTdB>feL
diff --git a/bin/pairToPair b/bin/pairToPair
index 3a2ede01fae21d0f18f07aadb92f5de4467dcd30..397f9f6d8a2e2430433fe9b6170024616bdb64c1 100755
GIT binary patch
delta 68
zcmV-K0K5Od_y)lE2C!fT5KQ!{4~fE9{0O^yqYpcD#<Oq+LJk28ld}{m0f@8S6oC5?
aEg(c?W?^+~bS?l1EopNJ0Jm=t0nw}IaT;;}
delta 68
zcmV-K0K5Od_y)lE2C!fT5X>Yi&Ux@E1-V4@Fw4<>>9cSKLJk29ld}{m0g1ET6oC5?
a2`wN*WoBV@Y;-OF2`y=J3Ab+$0nw}dq8lUt
diff --git a/bin/subtractBed b/bin/subtractBed
index 0a55fdcff738f36893c2b45e4abe1d2b4aec3765..4c1aa74f8248b8c67a03dc63a4aad1d205223aaf 100755
GIT binary patch
delta 53
zcmV-50LuU1zXjmG1+ZWS5T-<#9fNBLg+ET{(2+uAgR^i39t;5(laCTA0d}*x5@EcP
L9M2@PKhL3%QN9)Y
delta 53
zcmV-50LuU1zXjmG1+ZWS5ODTz$STQCWPze+G#~qg>$7kM9t;5)laCTA0e7>y5@EcP
L8qX!OK+m9%hY%NT
diff --git a/bin/windowBed b/bin/windowBed
index 13592c6ea49a61eff6ad93307e048b45adab25a2..37b7a59ff5ff18c88e40b386602942196af9323e 100755
GIT binary patch
delta 65
zcmV-H0KWf-;01`_1+ZWS5KH*X+5%un;#=VfamclmNwaVUt`Pw}lOGrx0W*_37%Blv
Xvt}6E!IMJTJ^=uef!aT_zuHNahTa=B
delta 65
zcmV-H0KWf-;01`_1+ZWS5cM>$H?0?jWM~X_BLC*f*t2j3t`Pw~lOGrx0W_047%Blw
Xvt}6E!IMDRKLH7ofZ9K^z}iTabz>U|
diff --git a/obj/closestMain.o b/obj/closestMain.o
index cd613d42842401f8eb5a2218914fe7a6182ce5b6..5d3d000363f35b5f4a6d20d9dc4276d19f09df1d 100644
GIT binary patch
delta 30
mcmaFi{K9!d9Sft*=6aS_oRhQo%r?*GyUES?b#tXuK05%$xC|Bm
delta 30
mcmaFi{K9!d9SfuG=6aS_oRc&7%r`IKyTQ%)ZF8kmK05%$#S9k!
diff --git a/obj/pairToPairMain.o b/obj/pairToPairMain.o
index 995e8a0d167962a2bb06116fb709596a9ac01a33..5048080f12f9914f50095592bd20a575a942c369 100644
GIT binary patch
delta 48
zcmdnuy2W+FCRRqC$?I8^H(z6o;1<+Xa7j%|EX^s=W8l=yEaqg`Y%iF|#W-{GLTO=k
E0F2-cz5oCK
delta 48
zcmdnuy2W+FCRRq?$?I8^H(z6o;1=Z6Rd7j7ODxSP(PQA$%`E2JY%iF|#W-v8LTO=k
E0ExH`$p8QV
diff --git a/obj/subtractMain.o b/obj/subtractMain.o
index c49f0af512ac0e9370392d200f459cb56afe4bf9..bdf6b3c4be116fd0a087855aae8b2bf9e98babcf 100644
GIT binary patch
delta 30
mcmaE0{=j@g9Sftx=6aSR?2}!1R5qvc9OPi!y;)OqI~xGB`U=|s
delta 30
mcmaE0{=j@g9Sfu6=6aSR?30~%R5xev9N=KwvsqJgI~xGC2MXK(
diff --git a/obj/windowMain.o b/obj/windowMain.o
index 67c34aee99078326c7973f3910ce356d4521ae36..251607d614f41c5d27f78732194e684e7779560c 100644
GIT binary patch
delta 44
zcmV+{0Mq}-V8~#wegu<F2OI%2lfMTev%UoD4wI@AJ^=ue=@UP*ClqlK0erKWCa(#8
CAP^b=
delta 46
zcmV+}0MY-*V8~#wegu;;2ON`%1{;%Y1_`si1nUlys1rW{36tm(KeH$la1sH1vzaEZ
E37Y~CqW}N^
diff --git a/src/closestBed/closestMain.cpp b/src/closestBed/closestMain.cpp
index e3f5da62..4ae7ae5d 100755
--- a/src/closestBed/closestMain.cpp
+++ b/src/closestBed/closestMain.cpp
@@ -107,7 +107,7 @@ void ShowHelp(void) {
cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << 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 << "\t feature (upstream or downstream) in BED B." << endl << endl;
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
diff --git a/src/pairToPair/pairToPairMain.cpp b/src/pairToPair/pairToPairMain.cpp
index 8bd9e338..e2e8a1b1 100755
--- a/src/pairToPair/pairToPairMain.cpp
+++ b/src/pairToPair/pairToPairMain.cpp
@@ -139,7 +139,7 @@ void ShowHelp(void) {
cerr << "\t\tneither\tReport overlaps if neither end of A overlaps B." << endl;
cerr << "\t\tboth\tReport overlaps if both ends of A overlap B." << endl;
- cerr << "\t\t\t- Default." << endl << endl;
+ cerr << "\t\t- Default." << endl << endl;
cerr << "\t-is\t" << "Ignore strands when searching for overlaps." << endl;
cerr << "\t\t- By default, strands are enforced." << endl << endl;
diff --git a/src/subtractBed/subtractMain.cpp b/src/subtractBed/subtractMain.cpp
index eccbc736..7889a386 100755
--- a/src/subtractBed/subtractMain.cpp
+++ b/src/subtractBed/subtractMain.cpp
@@ -112,7 +112,7 @@ void ShowHelp(void) {
cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
cerr << "Summary: Removes the portion(s) of an interval that is overlapped" << endl;
- cerr << "\t\t by another feature(s)." << endl << endl;
+ cerr << "\t by another feature(s)." << endl << endl;
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
diff --git a/src/windowBed/windowMain.cpp b/src/windowBed/windowMain.cpp
index 2507bc58..5346b653 100755
--- a/src/windowBed/windowMain.cpp
+++ b/src/windowBed/windowMain.cpp
@@ -167,8 +167,8 @@ void ShowHelp(void) {
cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << 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 << "\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 << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
--
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