merging changes from master (518c0a1f) · Commits · Chaos / chaos.juicer

AWS/scripts/LibraryComplexity.class

−133 B (4.42 KiB)

File changed.

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+1 −6

Changes for AWS/scripts/LibraryComplexity.java: 1 added line, 6 removed lines.
Original line number	Diff line number	Diff line
		@@ -109,8 +109,6 @@ class LibraryComplexity {
		decimalFormat.setMinimumFractionDigits(2);
		decimalFormat.setMaximumFractionDigits(2);

		long result2 = readPairsreadPairs/(2(readPairs-uniqueReadPairs));

		System.out.print("Unique Reads: " + NumberFormat.getInstance().format(uniqueReadPairs) + " ");
		if (totalReadPairs > 0) {
		System.out.println("(" + decimalFormat.format(uniqueReadPairs/(double)totalReadPairs) + ")");
		@@ -138,12 +136,9 @@ class LibraryComplexity {
		result = estimateLibrarySize(readPairs, uniqueReadPairs);
		}
		catch (NullPointerException e) {
		System.err.println("Library complexity undefined when total = " + readPairs + " and unique = " + uniqueReadPairs);
		return;
		result = 0;
		}
		System.out.println("Library Complexity Estimate: " + nf.format(result));
		// System.out.println("Library complexity (old): " + nf.format(result2));

		}

		/**

100755 → 100644

−133 B (4.42 KiB)

File changed.File mode changed from 100755 to 100644.

No diff preview for this file type.

+1 −6

Changes for CPU/common/LibraryComplexity.java: 1 added line, 6 removed lines.
Original line number	Diff line number	Diff line
		@@ -109,8 +109,6 @@ class LibraryComplexity {
		decimalFormat.setMinimumFractionDigits(2);
		decimalFormat.setMaximumFractionDigits(2);

		long result2 = readPairsreadPairs/(2(readPairs-uniqueReadPairs));

		System.out.print("Unique Reads: " + NumberFormat.getInstance().format(uniqueReadPairs) + " ");
		if (totalReadPairs > 0) {
		System.out.println("(" + decimalFormat.format(uniqueReadPairs/(double)totalReadPairs) + ")");
		@@ -138,12 +136,9 @@ class LibraryComplexity {
		result = estimateLibrarySize(readPairs, uniqueReadPairs);
		}
		catch (NullPointerException e) {
		System.err.println("Library complexity undefined when total = " + readPairs + " and unique = " + uniqueReadPairs);
		return;
		result = 0;
		}
		System.out.println("Library Complexity Estimate: " + nf.format(result));
		// System.out.println("Library complexity (old): " + nf.format(result2));

		}

		/**

+2 −2

Changes for CPU/common/countligations.sh: 2 added lines, 2 removed lines.
Original line number	Diff line number	Diff line
		@@ -27,10 +27,10 @@
		# Juicer version 1.5
		if [ "$usegzip" -eq 1 ]
		then
		num1=$(paste <(gunzip -c $file1) <(gunzip -c $file2) \| grep -c $ligation)
		num1=$(paste <(gunzip -c $file1) <(gunzip -c $file2) \| grep -cE $ligation)
		num2=$(gunzip -c $file1 \| wc -l \| awk '{print $1}')
		else
		num1=$(paste $file1 $file2 \| grep -c $ligation)
		num1=$(paste $file1 $file2 \| grep -cE $ligation)
		num2=$(wc -l $file1 \| awk '{print $1}')
		fi
		echo -ne "$num1 " > ${curr_ostem}_norm.txt.res.txt