Changeset 5837

Timestamp:

Feb 24, 2020, 3:40:08 PM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1218: Implement MIPs alignment

Re-designed the alignment and merge step.

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

@@ -296 +296 @@
       script.cmd("TrimOptionsAdapter=\""+align_trimmomaticOptions1+"\"");
       script.cmd("TrimOptionsQual=\""+align_trimmomaticOptions2+"\"");
+      script.cmd("NovoAlignOptions=\""+novoalign_options+"\"");
       
       script.newLine();
@@ -360 +361 @@
       script.newLine();
 
-      /*
+      script.comment("Run novoalign");
+      script.progress(40, "Aligning with novoalign");
       script.cmd("min_insert=$(awk 'NR == 1 || $3 - $2 < min {min = $3 - $2}END{print min - 1}' \"${AmpliconsBed}\")");
       script.cmd("max_insert=$(awk 'NR == 1 || $3 - $2 > max {max = $3 - $2}END{print max + 1}' \"${AmpliconsBed}\")");
-      script.comment("Run novoalign");
+      script.cmd("n=0");
       script.cmd("AlignedBams=''");
       script.cmd("for prefix in ${FastqPrefix[@]} ; do");
-      
-      String alignCmd = "./stderrwrap.sh ${NovoAlign}";
-      alignCmd += " -c ${NumThreads}";
-      alignCmd += " " + novoalign_options;
-      alignCmd += " -d ${NovoIndex} --tags MC,ZP -i PE ${min_insert}-${max_insert}";
-      alignCmd += " --amplicons ${AmpliconsBed}";
-      alignCmd += " 1 bam.aligned/${prefix}.novo_coverage.bed";
-      alignCmd += " -f bam.umi/${prefix}.bam";
-      alignCmd += " > bam.aligned/${prefix}.bam";
-      alignCmd += " 3> bam.aligned/${prefix}.novo.log";
-      
-      String sortCmd = "./stderrwrap.sh ${NovoSort}";
-      sortCmd += " -c ${NumThreads} -t . -i";
-      sortCmd += " -o bam.sorted/${prefix}.bam";
-      sortCmd += " bam.aligned/${prefix}.bam";
-      sortCmd += " 3> bam.sorted/${prefix}.novo.log";
-      
-      script.cmd("   " + alignCmd);
-      script.cmd("   " + sortCmd);
-      script.cmd("   AlignedBams=\"${AlignedBams} -INPUT bam.sorted/${prefix}.bam\"");
+      script.cmd("   n=$((n + 1))");
+      script.cmd("   novoalign \"${prefix}\" $n");
       script.cmd("done");
       script.newLine();
-      
       script.comment("Merge BAM files");
-      String mergeCmd = "./stdwrap.sh ./picard2 MergeSamFiles";
-      mergeCmd += " -SORT_ORDER coordinate -ASSUME_SORTED true";
-      mergeCmd += " ${AlignedBams}";
-      mergeCmd += " -OUTPUT bam.merged/novo.bam";
-      mergeCmd += " > mergesam.out";
-      script.cmd(mergeCmd);
-      script.newLine();
-
+      script.cmd("merge_bam");
+      script.newLine();
+      
+      /*
       script.comment("Re-header BAM files");
       script.cmd("${samtools} view -H bam.merged/novo.bam | grep -v \"^@SQ\" > header.sam");