Changeset 5839

Timestamp:

Feb 25, 2020, 9:34:29 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1218: Implement MIPs alignment

Re-designed the post-processing steps: re-header, split and mark duplicates.

File:

• extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/MipsAlignJobCreator.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/MipsAlignJobCreator.java

@@ -297 +297 @@
       script.cmd("TrimOptionsQual=\""+align_trimmomaticOptions2+"\"");
       script.cmd("NovoAlignOptions=\""+novoalign_options+"\"");
+      script.cmd("MarkDuplicatesOptions=\""+mark_duplicate_options+"\"");
       
       script.newLine();
@@ -375 +376 @@
       script.cmd("merge_bam");
       script.newLine();
-      
-      /*
-      script.comment("Re-header BAM files");
-      script.cmd("${samtools} view -H bam.merged/novo.bam | grep -v \"^@SQ\" > header.sam");
-      script.cmd("grep \"^@SQ\" ${GenomeDict} >> header.sam");
-      script.cmd("${samtools} reheader -P header.sam bam.merged/novo.bam > bam.merged/novo_reheaded.bam");
-      script.newLine();
-
-      script.comment("Separate concordant, discordant and unmapped read pairs");
-      script.cmd("${samtools} view -b -h -@ 2 -f 3 bam.merged/novo_reheaded.bam > bam.merged/concordant.bam");
-      script.cmd("${samtools} view -b -h -@ 2 -G 12 -F 2 bam.merged/novo_reheaded.bam > bam.merged/discordant.bam");
-      script.cmd("${samtools} view -b -h -@ 2 -f 12 bam.merged/novo_reheaded.bam > bam.merged/unmapped.bam");
-      
-      script.comment("Picard UmiAwareMarkDuplicatesWithMateCigar");
-      String markDupCmd = "./stdwrap.sh ./picard2 UmiAwareMarkDuplicatesWithMateCigar";
-      markDupCmd += " " + mark_duplicate_options;
-      markDupCmd += " -UMI_METRICS bam.final/concordant.umi_metrics.txt";
-      markDupCmd += " -METRICS_FILE bam.final/concordant.dedup_metrics.txt";
-      markDupCmd += " -INPUT bam.merged/concordant.bam";
-      markDupCmd += " -OUTPUT bam.final/concordant.bam";
-      markDupCmd += " >> markduplicates.out";
-      script.cmd(markDupCmd);
-      
-      markDupCmd = "./stdwrap.sh ./picard2 UmiAwareMarkDuplicatesWithMateCigar";
-      markDupCmd += " " + mark_duplicate_options;
-      markDupCmd += " -UMI_METRICS bam.final/discordant.umi_metrics.txt";
-      markDupCmd += " -METRICS_FILE bam.final/discordant.dedup_metrics.txt";
-      markDupCmd += " -INPUT bam.merged/discordant.bam";
-      markDupCmd += " -OUTPUT bam.final/discordant.bam";
-      markDupCmd += " >> markduplicates.out";
-      script.cmd(markDupCmd);
-      */
+
+      script.comment("Re-header BAM file");
+      script.progress(70, "Post-processing aligned BAM file");
+      script.cmd("reheader_bam");
+      script.newLine();
+      
+      script.comment("Split BAM file into concordant, discordant and unmapped");
+      script.cmd("split_bam");
+      script.newLine();
+
+      script.comment("Mark duplicates");
+      script.progress(80, "Marking duplicates");
+      script.cmd("mark_duplicates \"concordant\"");
+      script.cmd("mark_duplicates \"discordant\"");
+      script.newLine();
+
       /*
       script.progress(95, "Copying result files to project archive");