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ReadGroupProperties mk3 

-- Includes sequencing date
This commit is contained in:
Mark DePristo 2012-03-02 14:51:23 -05:00
parent fc1c0a9d8f
commit ba71b0aee4
1 changed files with 24 additions and 20 deletions
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44
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
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@ -36,13 +36,14 @@ import org.broadinstitute.sting.utils.Median;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.PrintStream;
import java.text.DateFormat;
import java.util.HashMap;
import java.util.Map;
/**
* Emits a GATKReport containing read group, sample, library, platform, center, paired end status,
* simple read type name (e.g. 2x76) median insert size and median read length for each read group
* in every provided BAM file
* Emits a GATKReport containing read group, sample, library, platform, center, sequencing data,
* paired end status, simple read type name (e.g. 2x76) median insert size and median read length
* for each read group in every provided BAM file
*
* Note that this walker stops when all read groups have been observed at least a few thousand times so that
* the median statistics are well determined. It is safe to run it WG and it'll finish in an appropriate
@ -61,23 +62,23 @@ import java.util.Map;
*
* <pre>
* ##:GATKReport.v0.2 ReadGroupProperties : Table of read group properties
* readgroup sample library platform center has.any.reads is.paired.end n.reads.analyzed simple.read.type median.read.length median.insert.size
* 20FUK.1 NA12878 Solexa-18483 illumina BI true true 10100 2x101 101 387
* 20FUK.2 NA12878 Solexa-18484 illumina BI true true 10115 2x101 101 415
* 20FUK.3 NA12878 Solexa-18483 illumina BI true true 10090 2x101 101 388
* 20FUK.4 NA12878 Solexa-18484 illumina BI true true 10081 2x101 101 415
* 20FUK.5 NA12878 Solexa-18483 illumina BI true true 10078 2x101 101 387
* 20FUK.6 NA12878 Solexa-18484 illumina BI true true 10072 2x101 101 415
* 20FUK.7 NA12878 Solexa-18483 illumina BI true true 10086 2x101 101 388
* 20FUK.8 NA12878 Solexa-18484 illumina BI true true 10097 2x101 101 415
* 20GAV.1 NA12878 Solexa-18483 illumina BI true true 10135 2x101 101 388
* 20GAV.2 NA12878 Solexa-18484 illumina BI true true 10172 2x101 101 415
* 20GAV.3 NA12878 Solexa-18483 illumina BI true true 10141 2x101 101 388
* 20GAV.4 NA12878 Solexa-18484 illumina BI true true 10251 2x101 101 416
* 20GAV.5 NA12878 Solexa-18483 illumina BI true true 10145 2x101 101 388
* 20GAV.6 NA12878 Solexa-18484 illumina BI true true 10184 2x101 101 415
* 20GAV.7 NA12878 Solexa-18483 illumina BI true true 10174 2x101 101 387
* 20GAV.8 NA12878 Solexa-18484 illumina BI true true 10141 2x101 101 414
* readgroup sample library platform center date has.any.reads is.paired.end n.reads.analyzed simple.read.type median.read.length median.insert.size
* 20FUK.1 NA12878 Solexa-18483 illumina BI 2/2/10 true true 498 2x101 101 386
* 20FUK.2 NA12878 Solexa-18484 illumina BI 2/2/10 true true 476 2x101 101 417
* 20FUK.3 NA12878 Solexa-18483 illumina BI 2/2/10 true true 407 2x101 101 387
* 20FUK.4 NA12878 Solexa-18484 illumina BI 2/2/10 true true 389 2x101 101 415
* 20FUK.5 NA12878 Solexa-18483 illumina BI 2/2/10 true true 433 2x101 101 386
* 20FUK.6 NA12878 Solexa-18484 illumina BI 2/2/10 true true 480 2x101 101 418
* 20FUK.7 NA12878 Solexa-18483 illumina BI 2/2/10 true true 450 2x101 101 386
* 20FUK.8 NA12878 Solexa-18484 illumina BI 2/2/10 true true 438 2x101 101 418
* 20GAV.1 NA12878 Solexa-18483 illumina BI 1/26/10 true true 490 2x101 101 391
* 20GAV.2 NA12878 Solexa-18484 illumina BI 1/26/10 true true 485 2x101 101 417
* 20GAV.3 NA12878 Solexa-18483 illumina BI 1/26/10 true true 460 2x101 101 392
* 20GAV.4 NA12878 Solexa-18484 illumina BI 1/26/10 true true 434 2x101 101 415
* 20GAV.5 NA12878 Solexa-18483 illumina BI 1/26/10 true true 479 2x101 101 389
* 20GAV.6 NA12878 Solexa-18484 illumina BI 1/26/10 true true 461 2x101 101 416
* 20GAV.7 NA12878 Solexa-18483 illumina BI 1/26/10 true true 509 2x101 101 386
* 20GAV.8 NA12878 Solexa-18484 illumina BI 1/26/10 true true 476 2x101 101 410 101 414
* </pre>
* </p>
*
@ -172,6 +173,7 @@ public class ReadGroupProperties extends ReadWalker<Integer, Integer> {
final GATKReport report = new GATKReport();
report.addTable(TABLE_NAME, "Table of read group properties");
GATKReportTable table = report.getTable(TABLE_NAME);
DateFormat dateFormatter = DateFormat.getDateInstance(DateFormat.SHORT);
table.addPrimaryKey("readgroup");
//* Emits a GATKReport containing read group, sample, library, platform, center, median insert size and
@ -180,6 +182,7 @@ public class ReadGroupProperties extends ReadWalker<Integer, Integer> {
table.addColumn("library", "NA");
table.addColumn("platform", "NA");
table.addColumn("center", "NA");
table.addColumn("date", "NA");
table.addColumn("has.any.reads", "false");
table.addColumn("is.paired.end", "false");
table.addColumn("n.reads.analyzed", "NA");
@ -200,6 +203,7 @@ public class ReadGroupProperties extends ReadWalker<Integer, Integer> {
table.set(rgID, "library", rg.getLibrary());
table.set(rgID, "platform", rg.getPlatform());
table.set(rgID, "center", rg.getSequencingCenter());
table.set(rgID, "date", dateFormatter.format(rg.getRunDate()));
table.set(rgID, "has.any.reads", hasAnyReads);
table.set(rgID, "is.paired.end", isPaired);
table.set(rgID, "n.reads.analyzed", info.nReadsSeen);