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[ADAM-1342] Update CLI docs after #1288 merged. #1343

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[ADAM-1342] Update CLI docs after #1288 merged. #1343

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40 changes: 20 additions & 20 deletions docs/source/50_cli.md
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Expand Up @@ -219,16 +219,6 @@ options]{#legacy-output}, `transformFeatures` has one optional argument:
Parquet), sets the number of partitions to load. If not provided, this is
chosen by Spark.

### flatten

Loads a Parquet file and rewrites the file as a new Parquet file with a flat
schema. This is useful if loading the data into a database that supports Parquet
but that does not support nested schemas. Takes two required arguments:

1. `INPUT`: The input path to a Parquet file.
2. `OUTPUT`: The path to save a Parquet file containing the input data, but
written using a flattened schema.

### mergeShards

A CLI tool for merging a [sharded legacy file](#legacy-output) that was written
Expand Down Expand Up @@ -278,7 +268,7 @@ following options:
These tools convert data between a legacy genomic file format and using ADAM's
schemas to store data in Parquet.

### vcf2adam, anno2adam, and adam2vcf
### vcf2adam and adam2vcf

These commands convert between VCF and Parquet using the Genotype and Variant
schemas.
Expand All @@ -303,15 +293,9 @@ Additionally, `vcf2adam` takes the following options:
if it would reduce the number of partitions to fewer than the number of
Spark executors. This may have a substantial performance cost, and will
invalidate any sort order.

`anno2adam` converts VCFs with annotated variants (i.e., the VCF INFO fields)
into Parquet using the VariantAnnotation schema. `anno2adam` takes the same two
required arguments as `vcf2adam`. `anno2adam` takes the [default
options](#default-args), and one additional option:

* `-annotations_to_join`: A path to an existing Parquet file of
VariantAnnotations. These two files are joined together, and the annotations
are merged.
* `-stringency`: Sets the validation stringency for conversion.
Defaults to `LENIENT.` See [validation stringency](#validation) for more
details.

`adam2vcf` takes two required arguments:

Expand All @@ -329,6 +313,22 @@ options](#default-args). Additionally, `adam2vcf` takes the following options:
contigs are ordered lexicographically. Conflicts with `-sort_on_save`.
* `-single`: Saves the VCF file as headerless shards, and then merges the
sharded files into a single VCF.
* `-stringency`: Sets the validation stringency for conversion.
Defaults to `LENIENT.` See [validation stringency](#validation) for more
details.

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Needs a line like

  • -stringency: Sets the validation stringency for various checks. Defaults to STRICT. See validation stringency for more details.

In these commands, the validation stringency is applied to the
individual variants and genotypes. If a variant or genotype fails validation, the
individual variant or genotype will be dropped (for lenient or silent validation,
under strict validation, conversion will fail). Header lines are not validated.
Due to a constraint imposed by the [htsjdk](https://github.com/samtools/htsjdk)
library, which we use to parse VCF files, user provided header lines that do not
match the header line definitions from the
[VCF 4.2](https://samtools.github.io/hts-specs/VCFv4.2.pdf) spec will be
overridden with the line definitions from the specification. Unfortunately, this
behavior cannot be disabled. If there is a user provided vs. spec mismatch in
format/info field count or type, this will likely cause validation failures
during conversion.

### fasta2adam and adam2fasta

Expand Down