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Slight improvements to allele caller interface; fixed problem with printing progress 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@260 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-02 16:44:12 +00:00
parent 20d4bcbb2e
commit 24e8581c30
5 changed files with 35 additions and 15 deletions
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35
doc/Genome Analysis TK plan.omniplan/contents.xml
View File

@ -28,9 +28,9 @@
<key>GanttGroupShading</key>
<false/>
<key>GanttVisibleRect</key>
<string>{{-35, 39}, {1025, 1033}}</string>
<string>{{-35, 124}, {1025, 1033}}</string>
<key>OutlineVisibleRect</key>
<string>{{0, 39}, {789, 1033}}</string>
<string>{{0, 124}, {789, 1033}}</string>
<key>ScaleWidths</key>
<dict>
<key>Automatic</key>
@ -86,7 +86,7 @@
<key>calendarController</key>
<dict>
<key>OutlineVisibleRect</key>
<string>{{0, 0}, {474, 720}}</string>
<string>{{0, 0}, {571, 830}}</string>
<key>activeColumnIdentifiers</key>
<array>
<string>IM</string>
@ -103,13 +103,13 @@
<key>Notes</key>
<real>20</real>
<key>Resource</key>
<real>339</real>
<real>436</real>
<key>Type</key>
<real>48</real>
</dict>
</dict>
<key>calendarSplit</key>
<real>0.67955440282821655</real>
<real>0.67960631847381592</real>
<key>columnWidths</key>
<dict>
<key>Effort</key>
@ -124,13 +124,13 @@
<key>dayWidth</key>
<real>54</real>
<key>resourceSplit</key>
<real>0.56749671697616577</real>
<real>0.56752324104309082</real>
<key>resourcesController</key>
<dict>
<key>DayWidth</key>
<real>25</real>
<key>OutlineVisibleRect</key>
<string>{{0, 0}, {645, 923}}</string>
<string>{{0, 0}, {776, 1033}}</string>
<key>ScaleWidths</key>
<dict>
<key>Automatic</key>
@ -153,7 +153,7 @@
<key>SelectedScale</key>
<string>Automatic</string>
<key>TimelineVisibleRect</key>
<string>{{-1467, 0}, {823, 923}}</string>
<string>{{-1467, 0}, {995, 1033}}</string>
<key>activeColumnIdentifiers</key>
<array>
<string>IM</string>
@ -171,7 +171,7 @@
<key>Notes</key>
<real>20</real>
<key>Resource</key>
<real>460</real>
<real>591</real>
<key>Type</key>
<real>64</real>
</dict>
@ -587,7 +587,7 @@
<key>taskDifferenceEngine</key>
<dict>
<key>nextId</key>
<integer>109</integer>
<integer>111</integer>
</dict>
<key>taskUserKeys</key>
<array/>
@ -1230,6 +1230,7 @@
<key>children</key>
<array>
<integer>18</integer>
<integer>109</integer>
<integer>19</integer>
<integer>37</integer>
<integer>33</integer>
@ -2378,6 +2379,18 @@
<key>workTime</key>
<real>8</real>
</dict>
<dict>
<key>effort</key>
<real>28800</real>
<key>objectId</key>
<integer>109</integer>
<key>task</key>
<string>Add mapping function from dict -&gt; dict so we can process 1KG data against HS_18 assembly</string>
<key>workSeconds</key>
<real>28800</real>
<key>workTime</key>
<real>8</real>
</dict>
</array>
<key>topResources</key>
<array>
@ -2388,7 +2401,7 @@
<integer>-1</integer>
</array>
<key>uuid</key>
<string>7E48C9E3-9ADF-4CC6-BB69-412F6D01690A</string>
<string>E50852A9-C0BE-452A-A050-4FF83DEF06D7</string>
<key>version</key>
<integer>2</integer>
</dict>

2
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
View File

@ -261,7 +261,7 @@ public abstract class TraversalEngine {
final long nRecords = this.nRecords;
final long curTime = System.currentTimeMillis();
final double elapsed = (curTime - startTime) / 1000.0;
//System.out.printf("Cur = %d, last print = %d%n", curTime, lastProgressPrintTime);
//System.out.printf("Cur = %d, last print = %d, elapsed=%.2f, nRecords=%d, met=%b%n", curTime, lastProgressPrintTime, elapsed, nRecords, maxElapsedIntervalForPrinting(curTime));
if (mustPrint || nRecords % N_RECORDS_TO_PRINT == 0 || maxElapsedIntervalForPrinting(curTime)) {
this.lastProgressPrintTime = curTime;

1
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
View File

@ -131,6 +131,7 @@ public class TraverseByLoci extends TraversalEngine {
done = true;
}
printProgress("loci", locus.getLocation());
}
done = interval != null && locus.getLocation().isPast(interval);

1
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java
View File

@ -86,6 +86,7 @@ public class TraverseByLociByReference extends TraverseByLoci {
done = true;
}
printProgress("loci", locus.getLocation());
refSite = refIter.next(); // update our location
}

11
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
View File

@ -399,8 +399,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
tokens = alleleFreq.location.split(":");
int current_offset = Integer.parseInt(tokens[1]);
if (inside_confident_ref_interval &&
((alleleFreq.lodVsRef > -5.0) || (current_offset != last_position_considered + 1)))
if (inside_confident_ref_interval &&
((alleleFreq.lodVsRef > -5.0) || (current_offset != last_position_considered + 1)) )
{
// No longer hom-ref, so output a ref line.
tokens = confident_ref_interval_start.split(":");
@ -469,7 +469,10 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
try
{
this.random = new java.util.Random(0);
this.output = new PrintStream(GFF_OUTPUT_FILE);
if ( GFF_OUTPUT_FILE.equals("-") )
this.output = out;
else
this.output = new PrintStream(GFF_OUTPUT_FILE);
}
catch (Exception e)
{
@ -510,6 +513,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
try
{
this.output.flush();
if ( ! GFF_OUTPUT_FILE.equals("-") )
this.output.close();
this.output.close();
}
catch (Exception e)