Command coverage ================ ``turbo-picard`` exposes the full Picard 3.4.0 command surface. Accelerated commands run natively in Rust when possible; every other Picard 3.4.0 command is delegated transparently to upstream Picard when it is installed or auto-discovered. List every upstream command with: .. code-block:: bash turbo-picard --list-commands Common command examples ----------------------- These examples cover the accelerated preprocessing and QC path. Check the machine-readable matrix below for the exact accelerated versus delegated split. .. code-block:: bash picard MarkDuplicates I=input.bam O=marked.bam M=metrics.txt picard SortSam I=input.bam O=coordinate.bam SORT_ORDER=coordinate picard CleanSam I=input.bam O=cleaned.bam picard MergeSamFiles I=lane1.bam I=lane2.bam O=merged.bam SORT_ORDER=coordinate picard BuildBamIndex I=coordinate.bam O=coordinate.bai picard SamToFastq I=input.bam FASTQ=r1.fastq SECOND_END_FASTQ=r2.fastq picard SamToFastq I=input.bam OUTPUT_PER_RG=true OUTPUT_DIR=fastq-by-rg picard FastqToSam F1=r1.fastq F2=r2.fastq O=unmapped.bam SM=sample RG=rg1 picard FastqToSam F1=reads_R1_001.fastq F2=reads_R2_001.fastq O=unmapped.bam SM=sample RG=rg1 USE_SEQUENTIAL_FASTQS=true picard ViewSam I=input.bam > view.sam picard ReplaceSamHeader I=input.bam O=reheadered.bam H=replacement-header.sam picard AddOrReplaceReadGroups I=input.bam O=rg.bam RGID=1 RGLB=lib RGPL=ILLUMINA RGPU=unit RGSM=sample picard CollectAlignmentSummaryMetrics I=input.bam O=alignment_metrics.txt picard CollectQualityYieldMetrics I=input.bam O=quality_yield_metrics.txt picard CreateSequenceDictionary R=reference.fa O=reference.dict picard NormalizeFasta I=reference.fa O=normalized.fa LINE_LENGTH=100 picard BedToIntervalList I=targets.bed O=targets.interval_list SD=reference.dict turbo-picard AccelerationStatus turbo-picard doctor turbo-picard explain MarkDuplicates I=input.bam O=marked.bam M=metrics.txt Metrics and repair examples --------------------------- .. code-block:: bash picard QualityScoreDistribution I=input.bam O=quality_distribution.txt CHART=quality_distribution.pdf picard MeanQualityByCycle I=input.bam O=mean_quality_by_cycle.txt CHART=mean_quality_by_cycle.pdf picard CollectBaseDistributionByCycle I=input.bam O=base_distribution.txt CHART=base_distribution.pdf picard CollectInsertSizeMetrics I=input.bam O=insert_size_metrics.txt H=insert_size_histogram.pdf picard CollectGcBiasMetrics I=input.bam O=gc_bias_detail.txt S=gc_bias_summary.txt CHART=gc_bias.pdf R=reference.fa picard CollectHsMetrics I=input.bam O=hs_metrics.txt BAIT=baits.interval_list TARGET=targets.interval_list R=reference.fa picard CollectMultipleMetrics I=input.bam O=multiple_metrics PROGRAM=CollectInsertSizeMetrics picard CollectWgsMetrics I=input.bam O=wgs_metrics.txt R=reference.fa COUNT_UNPAIRED=true picard CollectWgsMetrics I=input.bam O=wgs_metrics.fast.txt R=reference.fa COUNT_UNPAIRED=true USE_FAST_ALGORITHM=true picard FixMateInformation I=queryname.bam O=fixed.bam ASSUME_SORTED=true SORT_ORDER=queryname picard RevertSam I=aligned.bam O=unmapped.bam picard SetNmMdAndUqTags I=coordinate.bam O=tagged.bam R=reference.fa picard ValidateSamFile I=input.bam MODE=SUMMARY VCF and interval examples ------------------------- .. code-block:: bash picard UpdateVcfSequenceDictionary I=input.vcf O=updated.vcf SD=reference.dict CREATE_INDEX=true picard GatherVcfs I=shard1.vcf I=shard2.vcf O=gathered.vcf CREATE_INDEX=true picard SortVcf I=unsorted.vcf O=sorted.vcf SD=reference.dict CREATE_INDEX=true picard MergeVcfs I=batch1.vcf I=batch2.vcf O=merged.vcf CREATE_INDEX=true picard LiftoverVcf I=input.vcf O=lifted.vcf CHAIN=build.chain REJECT=rejected.vcf R=target.fa picard IntervalListTools I=a.interval_list I=b.interval_list O=merged.interval_list ACTION=CONCAT SORT=true UNIQUE=true Machine-readable coverage ------------------------- The canonical command matrix lives in ``docs/command-matrix.yml``. It records the current status, parity script, native scope, and fallback scope for each Picard 3.4.0 command plus turbo-only utilities such as ``AccelerationStatus``, ``doctor``, and ``explain``. Current matrix status summary: * ``35 accelerated`` commands with native or partial-native Rust implementations * ``89 delegated`` Picard 3.4.0 commands forwarded to upstream Picard Accelerated command status: * ``AddOrReplaceReadGroups``: ``native`` * ``AccelerationStatus``: ``native`` * ``BedToIntervalList``: ``native`` * ``BuildBamIndex``: ``native`` * ``CleanSam``: ``partial-native`` * ``CollectAlignmentSummaryMetrics``: ``partial-native`` * ``CollectBaseDistributionByCycle``: ``partial-native`` * ``CollectGcBiasMetrics``: ``partial-native`` * ``CollectQualityYieldMetrics``: ``native`` * ``CollectWgsMetrics``: ``partial-native``. ``INCLUDE_BQ_HISTOGRAM`` defaults to ``false`` to match Picard 3.4.0 histogram output. ``USE_FAST_ALGORITHM=true`` stays native and defaults ``SAMPLE_SIZE`` to ``0`` unless it is set explicitly. ``TURBO_PICARD_WGS_FAST_DEFAULT=true`` applies that sample-size default when the command line does not set ``USE_FAST_ALGORITHM``. * ``doctor``: ``native`` * ``explain``: ``native`` * ``CreateSequenceDictionary``: ``native`` * ``FastqToSam``: ``partial-native`` * ``GatherVcfs``: ``partial-native`` * ``MarkDuplicates``: ``partial-native`` * ``MergeSamFiles``: ``partial-native`` * ``MergeVcfs``: ``partial-native`` * ``MeanQualityByCycle``: ``partial-native`` * ``NormalizeFasta``: ``native`` * ``QualityScoreDistribution``: ``partial-native`` * ``ReplaceSamHeader``: ``partial-native`` * ``SamToFastq``: ``partial-native`` * ``SortSam``: ``partial-native`` * ``SortVcf``: ``partial-native`` * ``UpdateVcfSequenceDictionary``: ``partial-native`` * ``ViewSam``: ``partial-native`` * ``CollectInsertSizeMetrics``: ``partial-native`` * ``CollectMultipleMetrics``: ``partial-native`` * ``FixMateInformation``: ``partial-native`` * ``IntervalListTools``: ``partial-native`` * ``LiftoverVcf``: ``partial-native`` * ``RevertSam``: ``partial-native`` * ``SetNmMdAndUqTags``: ``partial-native`` * ``ValidateSamFile``: ``partial-native`` .. literalinclude:: command-matrix.yml :language: yaml