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Merge pull request #968 from aidenlab/final_stats_update
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Sstats update
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@sa501428
sa501428 committed Sep 20, 2021
2 parents e983324 + 2b0e323 commit 1bf3dfb
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Showing 2 changed files with 59 additions and 14 deletions.
2 changes: 1 addition & 1 deletion src/juicebox/HiCGlobals.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
*/
public class HiCGlobals {

public static final String versionNum = "2.13.05";
public static final String versionNum = "2.13.06";
public static final String juiceboxTitle = "[Juicebox " + versionNum + "] Hi-C Map ";

// MainWindow variables
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71 changes: 58 additions & 13 deletions src/juicebox/tools/utils/original/stats/StatisticsContainer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,9 @@ public class StatisticsContainer {
private final static float CONVERGENCE_THRESHOLD = 0.01f;
private final static int CONVERGENCE_REGION = 3;
private final static int SEQ_INDEX = 0, DUPS_INDEX = 1, UNIQUE_INDEX = 2;
private final static int LC_INDEX = 3, SINGLE_ALIGNMENT_INDEX = 4, NUM_TO_READ = 5;
private final static int LC_INDEX = 3, SINGLE_ALIGNMENT_INDEX = 4;
private final static int SINGLE_ALIGN_DUPS_INDEX = 5, SINGLE_ALIGN_UNIQUE_INDEX = 6;
private final static int NUM_TO_READ = 7;
private final NumberFormat nf = NumberFormat.getNumberInstance(Locale.US);

//Variables for calculating statistics
Expand Down Expand Up @@ -167,10 +169,10 @@ public void outputStatsFile(List<String> statsFiles) {
writeLibComplexityIfNeeded(valsWereFound, valsFound, statsOut);
if (unique == 0) unique = 1;
writeOut(statsOut, "Intra-fragment Reads: ", valsWereFound, intraFragment[i], valsFound, unique, true);
if (!isUTLibrary(valsWereFound, valsFound, underMapQ[i])) {
attemptMapqCorrection(valsWereFound, valsFound, underMapQ, unique, i);
writeOut(statsOut, "Below MAPQ Threshold: ", valsWereFound, underMapQ[i], valsFound, unique, true);
}
//if (!isUTLibrary(valsWereFound, valsFound, underMapQ[i])) {
attemptMapqCorrection(valsWereFound, valsFound, underMapQ, unique, i);
writeOut(statsOut, "Below MAPQ Threshold: ", valsWereFound, underMapQ[i], valsFound, unique, true);
//}
writeOut(statsOut, "Hi-C Contacts: ", valsWereFound, totalCurrent[i], valsFound, unique, false);
//writeOut(statsOut, " Ligation Motif Present: ", valsWereFound, ligation[i], valsFound, unique, true);
appendPairTypeStatsOutputToFile(i, statsOut);
Expand All @@ -196,12 +198,40 @@ private boolean isUTLibrary(boolean[] valsWereFound, long[] valsFound, long belo
}

private void writeLibComplexityIfNeeded(boolean[] valsWereFound, long[] valsFound, BufferedWriter statsOut) throws IOException {
if (!valsWereFound[LC_INDEX] && valsWereFound[UNIQUE_INDEX] && valsWereFound[DUPS_INDEX]) {
long result = LibraryComplexity.estimateLibrarySize(valsFound[DUPS_INDEX], valsFound[UNIQUE_INDEX]);
if (result > 0) {
statsOut.write("Library Complexity Estimate: " + commify(result) + "\n");
} else {
statsOut.write("Library Complexity Estimate: N/A\n");
if (!valsWereFound[LC_INDEX]) {
boolean isUTExperiment = false;
long lcTotal = 0L;
if (valsWereFound[SINGLE_ALIGN_UNIQUE_INDEX] && valsWereFound[SINGLE_ALIGN_DUPS_INDEX]) {
long resultLC1 = LibraryComplexity.estimateLibrarySize(valsFound[SINGLE_ALIGN_DUPS_INDEX], valsFound[SINGLE_ALIGN_UNIQUE_INDEX]);
isUTExperiment = true;
if (resultLC1 > 0) {
lcTotal += resultLC1;
statsOut.write("Library Complexity Estimate (1 alignment)*: " + commify(resultLC1) + "\n");
} else {
statsOut.write("Library Complexity Estimate (1 alignment)*: N/A\n");
}
}

if (valsWereFound[UNIQUE_INDEX] && valsWereFound[DUPS_INDEX]) {
long resultLC2 = LibraryComplexity.estimateLibrarySize(valsFound[DUPS_INDEX], valsFound[UNIQUE_INDEX]);
String description = "";
if (isUTExperiment) {
description = " (2 alignments)";
}
if (resultLC2 > 0) {
lcTotal += resultLC2;
statsOut.write("Library Complexity Estimate" + description + "*: " + commify(resultLC2) + "\n");
} else {
statsOut.write("Library Complexity Estimate" + description + "*: N/A\n");
}
}

if (isUTExperiment) {
if (lcTotal > 0) {
statsOut.write("Library Complexity Estimate (1+2 above)*: " + commify(lcTotal) + "\n");
} else {
statsOut.write("Library Complexity Estimate (1+2 above)*: N/A\n");
}
}
}
}
Expand All @@ -218,9 +248,17 @@ private void attempReadingDataFromExistingFile(boolean[] valsWereFound, long[] v
if (statsData.contains("sequenced")) {
populateFoundVals(statsData, valsWereFound, valsFound, SEQ_INDEX);
} else if (statsData.contains("unique")) {
populateFoundVals(statsData, valsWereFound, valsFound, UNIQUE_INDEX);
if (isSingleAlignment(statsData)) {
populateFoundVals(statsData, valsWereFound, valsFound, SINGLE_ALIGN_UNIQUE_INDEX);
} else {
populateFoundVals(statsData, valsWereFound, valsFound, UNIQUE_INDEX);
}
} else if (statsData.contains("duplicate") && !statsData.contains("optical")) {
populateFoundVals(statsData, valsWereFound, valsFound, DUPS_INDEX);
if (isSingleAlignment(statsData)) {
populateFoundVals(statsData, valsWereFound, valsFound, SINGLE_ALIGN_DUPS_INDEX);
} else {
populateFoundVals(statsData, valsWereFound, valsFound, DUPS_INDEX);
}
} else if (statsData.contains("complexity")) {
populateFoundVals(statsData, valsWereFound, valsFound, LC_INDEX);
} else if (statsData.contains("single") && statsData.contains("alignment")) {
Expand All @@ -235,6 +273,13 @@ private void attempReadingDataFromExistingFile(boolean[] valsWereFound, long[] v
}
}

private boolean isSingleAlignment(String text) {
String[] tokens = text.split(":");
String description = tokens[0].toLowerCase();
return (description.contains("1") || description.contains("one")) &&
description.contains("alignment");
}

private void populateFoundVals(String statsData, boolean[] valsWereFound, long[] valsFound, int index) {
if (!valsWereFound[index]) {
valsWereFound[index] = true;
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