## htsjdk.samtools.metrics.StringHeader
# au.edu.wehi.idsv.Idsv WORKER_THREADS=1 INPUT=[test.bam] INPUT_READ_PAIR_MAX_CONCORDANT_FRAGMENT_SIZE=[650] INPUT_READ_PAIR_MIN_CONCORDANT_FRAGMENT_SIZE=[350] OUTPUT=debug.vcf REFERENCE=/home/users/allstaff/cameron.d/reference_genomes/human/hg19.fa SCRIPT=realign.sh PER_CHR=false WORKING_DIR=. MIN_INDEL_SIZE=0 TMP_DIR=[.] VERBOSITY=DEBUG    STEPS=[CALCULATE_METRICS, EXTRACT_SOFT_CLIPS, EXTRACT_READ_PAIRS, ASSEMBLE_BREAKENDS, REALIGN_SOFT_CLIPS, REALIGN_ASSEMLIES, SORT_REALIGNED_SOFT_CLIPS, SORT_REALIGNED_ASSEMBLIES, CALL_STRUCTURAL_VARIANTS, ANNOTATE_VARIANTS] READ_PAIR_CONCORDANT_PERCENT=0.995 SOFT_CLIP_MIN_LENGTH=4 READ_PAIR_ANCHOR_MIN_MAPQ=5 SOFT_CLIP_MIN_MAPQ=5 READ_PAIR_MIN_ENTROPY=0.5 SOFT_CLIP_MIN_ENTROPY=0.5 SOFT_CLIP_MIN_ANCHOR_PERCENT_IDENTITY=95.0 SOFT_CLIP_MIN_BASE_QUALITY=5.0 ADAPTER_SEQUENCE=[AGATCGGAAGAG, ATGGAATTCTCG, CTGTCTCTTATA] ASSEMBLY_ALGORITHM=Positional ASSEMBLY_DEBRUIJN_KMER=25 ASSEMBLY_INCLUDE_REMOTE_SOFT_CLIPS=true ASSEMBLY_DEBRUIJN_MAX_PATH_COLLAPSE_BASE_MISMATCHES=4 ASSEMBLY_DEBRUIJN_COLLAPSE_BUBBLES_ONLY=true ASSEMBLY_DEBRUIJN_ALLOW_REFERENCE_KMER_RESUSE=true ASSEMBLY_DEBRUIJN_MAX_CONTIGS_PER_ITERATION=1024 ASSEMBLY_DEBRUIJN_SUBGRAPH_BRANCHING_FACTOR=16 ASSEMBLY_DEBRUIJN_SUBGRAPH_ASSEMBLY_FRAGMENT_DELAY=4.0 REALIGNMENT_MIN_BREAKEND_LENGTH=25 REALIGNMENT_MIN_BASE_QUALITY=5.0 REALIGNMENT_MAPQ_UNIQUE_THRESHOLD=10 ASSEMBLY_REALIGNMENT_ITERATORS=1 BREAKEND_MARGIN=10 MAX_COVERAGE=100000 SOMATIC_THRESHOLD=0.001 CALL_ONLY_ASSEMBLIES=false MIN_SCORE=25.0 VCF41_COMPATIBLE=true QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Aug 04 16:36:49 AEST 2015

## METRICS CLASS	picard.analysis.InsertSizeMetrics
MEDIAN_INSERT_SIZE	MEDIAN_ABSOLUTE_DEVIATION	MIN_INSERT_SIZE	MAX_INSERT_SIZE	MEAN_INSERT_SIZE	STANDARD_DEVIATION	READ_PAIRS	PAIR_ORIENTATION	WIDTH_OF_10_PERCENT	WIDTH_OF_20_PERCENT	WIDTH_OF_30_PERCENT	WIDTH_OF_40_PERCENT	WIDTH_OF_50_PERCENT	WIDTH_OF_60_PERCENT	WIDTH_OF_70_PERCENT	WIDTH_OF_80_PERCENT	WIDTH_OF_90_PERCENT	WIDTH_OF_99_PERCENT	SAMPLE	LIBRARY	READ_GROUP
498	35	329	70638378	496.965688	49.900621	2216	FR	13	25	39	55	71	85	105	131	165	255			
37074656	32	37074528	37074816	?	-0	301	RF	11	25	41	53	65	83	103	125	171	237			
12320959	583	12320179	91412506	?	-0	214	TANDEM	161	355	659	907	1161	1469	90344217	90345031	90345461	145989647			

## HISTOGRAM	java.lang.Integer
insert_size	All_Reads.fr_count
329	1
344	1
350	1
354	1
358	2
371	2
373	2
376	1
377	1
378	1
380	3
381	1
382	1
383	1
384	2
386	2
387	2
388	4
392	4
393	2
395	2
396	2
397	2
399	3
400	4
401	3
402	2
403	3
405	5
406	4
407	2
408	3
409	6
410	2
411	5
412	5
413	5
414	5
415	6
416	5
417	5
418	5
419	6
420	10
421	6
422	7
423	8
424	4
425	11
426	5
427	8
428	7
429	6
430	8
431	10
432	6
433	9
434	6
435	8
436	8
437	7
438	15
439	6
440	11
441	9
442	7
443	11
444	12
445	14
446	8
447	6
448	10
449	10
450	19
451	16
452	19
453	10
454	12
455	17
456	12
457	16
458	10
459	16
460	17
461	12
462	10
463	17
464	16
465	17
466	13
467	16
468	10
469	14
470	16
471	11
472	9
473	11
474	18
475	16
476	14
477	18
478	12
479	15
480	11
481	16
482	21
483	13
484	11
485	18
486	22
487	15
488	15
489	18
490	20
491	16
492	16
493	15
494	26
495	11
496	20
497	15
498	21
499	23
500	20
501	30
502	13
503	18
504	16
505	17
506	22
507	22
508	16
509	11
510	25
511	18
512	18
513	16
514	16
515	20
516	15
517	15
518	20
519	20
520	12
521	10
522	13
523	17
524	7
525	10
526	23
527	11
528	11
529	14
530	20
531	7
532	14
533	13
534	17
535	15
536	16
537	10
538	14
539	12
540	20
541	13
542	9
543	12
544	10
545	5
546	9
547	9
548	10
549	8
550	12
551	5
552	7
553	10
554	12
555	8
556	12
557	6
558	12
559	7
560	6
561	12
562	4
563	5
564	3
565	10
566	10
567	7
568	8
569	3
570	5
571	8
572	5
573	6
574	3
575	4
576	9
577	2
578	5
579	8
580	5
581	6
582	6
583	1
584	4
585	4
586	4
587	4
588	2
589	3
590	2
591	3
593	4
594	3
595	2
596	3
597	3
598	2
600	1
601	4
602	2
603	1
604	4
605	2
606	1
607	1
609	2
610	2
611	2
612	1
613	2
614	1
616	1
617	1
618	1
621	1
622	3
623	2
624	1
626	1
628	2
629	1
631	1
633	1
634	1
635	1
637	1
639	1
646	1
657	1
658	1
662	1
680	1

