From 7ae8a4d485ae26a88611828049759aab678d6cdd Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Sun, 4 Jul 2010 21:15:58 -0400
Subject: [PATCH] Added slop to filename when using -slop in bedToIgv.
---
src/bedToIgv/bedToIgv.cpp | 15 ++++++++-------
1 file changed, 8 insertions(+), 7 deletions(-)
diff --git a/src/bedToIgv/bedToIgv.cpp b/src/bedToIgv/bedToIgv.cpp
index 5c116029..4df564dd 100755
--- a/src/bedToIgv/bedToIgv.cpp
+++ b/src/bedToIgv/bedToIgv.cpp
@@ -236,19 +236,20 @@ void ProcessBed(istream &bedInput, BedFile *bed, string path, string sortType, s
while ((bedStatus = bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) {
if (bedStatus == BED_VALID) {
- string locus, filename;
- locus = bedEntry.chrom + ":" + ToString(bedEntry.start - slop) + "-" + ToString(bedEntry.end + slop);
+ string filename = bedEntry.chrom + ":" + ToString(bedEntry.start) + "-" + ToString(bedEntry.end);
+ string locus = bedEntry.chrom + ":" + ToString(bedEntry.start - slop) + "-" + ToString(bedEntry.end + slop);
- if (useNames == false)
- filename = locus;
- else {
+ if (useNames == true) {
if (bedEntry.name.empty() == false)
- filename = bedEntry.name;
+ filename = filename + "_" + bedEntry.name;
else {
cerr << "Error: You requested that filenames be based upon the name field. However, it appears to be empty. Exiting!" << endl;
exit (1);
}
}
+ if (slop > 0) {
+ filename = filename + "_" + "slop" + ToString(slop);
+ }
// goto
cout << "goto " << locus << endl;
@@ -262,7 +263,7 @@ void ProcessBed(istream &bedInput, BedFile *bed, string path, string sortType, s
// snapshot
cout << "snapshot " << filename << "." << imageType << endl;
-
+
// reset
bedEntry = nullBed;
}
--
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