Cheatsheet

Every exported name in the deck, by module. A function's return type is not declared in Jennifer, so it is given in the description.

For the reasoning behind these calls, start from the topic pages - this page is the index, not the explanation.

`core`

Shared primitives the rest of the deck is built on: error construction, Go-speed counting, tab-delimited field access.

Constants

constant	type	value	description
`core.ERROR_KIND`	`string`	`"ngs"`	Deck-wide error kind prefix, so a caller can match on `$e.kind`.
`core.TAB`	`string`	`"\t"`	Tab, the field separator every text format in this deck uses.

Functions

function	description
`core.fail(what as string, message as string)`	Raise a deck error with a stable kind.
`core.countIn(haystack as string, needle as string)`	Count non-overlapping occurrences of `needle` in `haystack`.
`core.parseInt(what as string, label as string, raw as string)`	Parse an integer field, reporting a malformed value as a deck error.
`core.parseFloat(what as string, label as string, raw as string)`	Parse a float field, reporting a malformed value as a deck error.
`core.reraise(what as string, line as string, e as Error)`	Re-raise a parse failure as a deck error naming the record it came from.
`core.splitTab(line as string)`	Split a tab-delimited line into its fields.
`core.field(fields as list of string, i as int, fallback as string)`	Field `i` of `fields`, or `fallback` when the column is absent.
`core.intField(what as string, fields as list of string, i as int, fallback as int)`	Integer field `i`, or `fallback` when absent, empty or a placeholder dot.
`core.floatField(what as string, fields as list of string, i as int, fallback as float)`	Float field `i`, or `fallback` when absent, empty or a placeholder dot.
`core.isSkippable(line as string, marker as string)`	Whether a line should be skipped by a record reader: empty or a comment.
`core.padNum(n as int, width as int)`	Left-pad an integer with zeros to `width`, for building sortable string keys.
`core.shellQuote(s as string)`	Quote a string for safe inclusion in a POSIX `sh -c` command line.
`core.reverseComplement(seq as string)`	Reverse complement of a DNA sequence.
`core.complementBase(b as string)`	Complement of a single nucleotide character.
`core.gcCount(seq as string)`	G+C count of a sequence, counted at Go speed.
`core.nCount(seq as string)`	Ambiguous-base (N) count of a sequence, counted at Go speed.
`core.hasTool(name as string)`	Whether an executable is on `PATH`.
`core.sameFile(a as string, b as string)`	Whether two paths resolve to the same file.

`source`

Streaming line sources and sinks, with transparent gzip in both directions.

Types

type	kind	description
`source.Source`	struct	An open line source. Treat it as an opaque handle and pass it around by value: the `fs.File` and `os.Process` fields are registry handles, so copies share the same underlying stream.
`source.Sink`	struct	An open line sink, the write-side counterpart of `Source`.

Constants

constant	type	value	description
`source.GZIP_MAGIC1`	`int`	`0x1f`	First byte of the gzip magic number (RFC 1952).
`source.GZIP_MAGIC2`	`int`	`0x8b`	Second byte of the gzip magic number (RFC 1952).

Functions

function	description
`source.isGzip(path as string)`	Whether a file starts with the gzip magic number.
`source.open(path as string)`	Open a file for streaming line reads, decompressing gzip transparently.
`source.openPlain(path as string)`	Open an uncompressed file for streaming line reads.
`source.openStdin()`	Open standard input as a line source, so the deck composes with Unix pipes.
`source.openGzip(path as string)`	Open a gzipped file for streaming line reads at constant memory.
`source.openGzipBuffered(path as string)`	Open a gzipped file by decompressing it whole, for hosts without `exec`.
`source.hasNext(s as Source)`	Whether another line can be read from the source.
`source.nextLine(s as Source)`	Read the next line, with its line terminator stripped.
`source.close(s as Source)`	Close a source and release its child process and temporary files.
`source.closeStrict(s as Source)`	Close a fully-consumed source, raising if its decompressor failed.
`source.create(path as string)`	Open a file for streaming line writes, gzip-compressing when the name ends in `.gz`.
`source.createPlain(path as string)`	Open an uncompressed file for streaming line writes.
`source.createGzip(path as string)`	Open a gzip-compressed file for streaming line writes at constant memory.
`source.writeText(k as Sink, text as string)`	Write text to a sink verbatim, adding no line terminator.
`source.writeLine(k as Sink, line as string)`	Write one line to a sink, appending a newline.
`source.closeSink(k as Sink)`	Close a sink, flush it and wait for its compressor to finish.

`fastq`

FASTQ records, streaming reader and writer, per-record accessors.

Types

type	kind	description
`fastq.Read`	struct	One FASTQ record.
`fastq.Reader`	struct	A streaming FASTQ cursor.

Constants

constant	type	value	description
`fastq.PHRED33`	`int`	`33`	Sanger / Illumina 1.8+ quality offset; the modern default.
`fastq.PHRED64`	`int`	`64`	Legacy Illumina 1.3-1.7 quality offset.

Functions

function	description
`fastq.open(path as string)`	Open a FASTQ file for streaming, decompressing gzip transparently.
`fastq.openStdin()`	Open standard input as a FASTQ stream, for use in Unix pipes.
`fastq.hasNext(r as Reader)`	Whether another record is available.
`fastq.next(r as Reader)`	Read the next record.
`fastq.close(r as Reader)`	Close the reader and release its decompressor.
`fastq.closeStrict(r as Reader)`	Close a fully-consumed reader, raising if its decompressor failed.
`fastq.parse(header as string, seq as string, plus as string, qual as string)`	Build a record from its four raw lines, validating the FASTQ shape.
`fastq.format(rec as Read)`	Render a record back to its four-line FASTQ text, newline-terminated.
`fastq.toFasta(rec as Read)`	Render a record as two-line FASTA text, newline-terminated.
`fastq.headerOf(rec as Read)`	The full header text of a record: id plus description when present.
`fastq.write(k as source.Sink, rec as Read)`	Write a record to a sink as FASTQ.
`fastq.length(rec as Read)`	Read length in bases.
`fastq.qualities(rec as Read, offset as int)`	Decode the quality string to Phred scores.
`fastq.meanQuality(rec as Read, offset as int)`	Mean Phred quality of a record.
`fastq.minQuality(rec as Read, offset as int)`	Lowest Phred score in a record.
`fastq.gcPercent(rec as Read)`	G+C content of a record as a percentage, counted at Go speed.
`fastq.ambiguousCount(rec as Read)`	Number of ambiguous (N) bases in a record, counted at Go speed.
`fastq.subseq(rec as Read, start as int, end as int)`	A sub-range of a record, slicing sequence and quality together.
`fastq.reverseComplement(rec as Read)`	Reverse complement of a record, with the quality string reversed to match.

`bed`

Streaming BED reading and writing, straight onto the interval engine.

Types

type	kind	description
`bed.Reader`	struct	A streaming BED cursor.
`bed.Next`	enum	The result of advancing a BED cursor: either a feature or end-of-stream.

Constants

constant	type	value	description
`bed.MISSING`	`string`	`"."`	Placeholder written for an absent name or strand.

Functions

function	description
`bed.open(path as string)`	Open a BED file for streaming, decompressing gzip transparently.
`bed.openStdin()`	Open standard input as a BED stream.
`bed.next(r as Reader)`	Advance the cursor to the next feature, skipping blank, comment, `track` and `browser` lines.
`bed.close(r as Reader)`	Close the cursor and release its decompressor.
`bed.closeStrict(r as Reader)`	Close a fully-consumed cursor, raising if its decompressor failed.
`bed.parse(line as string)`	Parse one BED line into an interval.
`bed.format(iv as intervals.Interval)`	Render an interval as a six-column BED line.
`bed.readAll(path as string)`	Read a whole BED file into memory.
`bed.writeAll(path as string, ivs as list of intervals.Interval)`	Write intervals to a BED file, gzipping when the name ends in `.gz`.
`bed.write(k as source.Sink, iv as intervals.Interval)`	Write one interval to an already-open sink.

`gff`

Streaming GFF3 and GTF reading and writing, with attribute parsing in both styles.

Types

type	kind	description
`gff.Feature`	struct	One GFF3 or GTF feature.
`gff.Reader`	struct	A streaming GFF/GTF cursor.
`gff.Next`	enum	The result of advancing a GFF cursor.

Constants

constant	type	value	description
`gff.MISSING`	`string`	`"."`	Placeholder used for an absent column.
`gff.STYLE_GFF3`	`string`	`"gff3"`	Attribute style: `key=value;` pairs, percent-escaped.
`gff.STYLE_GTF`	`string`	`"gtf"`	Attribute style: `key "value";` pairs.

Functions

function	description
`gff.open(path as string)`	Open a GFF3 or GTF file for streaming, decompressing gzip transparently.
`gff.openStdin()`	Open standard input as a GFF/GTF stream.
`gff.next(r as Reader)`	Advance the cursor to the next feature.
`gff.close(r as Reader)`	Close the cursor and release its decompressor.
`gff.closeStrict(r as Reader)`	Close a fully-consumed cursor, raising if its decompressor failed.
`gff.parse(line as string)`	Parse one GFF3 or GTF record.
`gff.parseAttributes(text as string)`	Parse a ninth-column attribute string in either GFF3 or GTF style.
`gff.styleOf(text as string)`	Which attribute style a ninth column uses.
`gff.attribute(f as Feature, key as string, fallback as string)`	Read an attribute, or a fallback when it is absent.
`gff.identifier(f as Feature)`	The feature's identifier: GFF3 `ID`, else GTF `transcript_id`, else `gene_id`.
`gff.name(f as Feature)`	The feature's display name: GFF3 `Name`, else `gene_name`, else `identifier`.
`gff.toInterval(f as Feature)`	Convert a feature to a half-open interval for the interval engine.
`gff.fromInterval(iv as intervals.Interval, origin as string, kind as string)`	Build a feature from a half-open interval, converting back to 1-based.
`gff.format(f as Feature, style as string)`	Render a feature as a nine-column record.
`gff.formatAttributes(attrs as map of string to string, style as string)`	Render an attribute map in GFF3 or GTF style.
`gff.readAll(path as string)`	Read a whole annotation file into memory.
`gff.readIntervals(path as string, kind as string)`	Read an annotation file directly as half-open intervals.

`sam`

Streaming SAM reading and writing, FLAG and CIGAR handling.

Types

type	kind	description
`sam.Record`	struct	One SAM alignment record.
`sam.CigarOp`	struct	One CIGAR operation.
`sam.Reader`	struct	A streaming SAM cursor, carrying the file's header block.
`sam.Next`	enum	The result of advancing a SAM cursor.

Constants

constant	type	value	description
`sam.FLAG_PAIRED`	`int`	`0x1`	Read is paired in sequencing.
`sam.FLAG_PROPER_PAIR`	`int`	`0x2`	Each segment is properly aligned according to the aligner.
`sam.FLAG_UNMAPPED`	`int`	`0x4`	This segment is unmapped.
`sam.FLAG_MATE_UNMAPPED`	`int`	`0x8`	The mate segment is unmapped.
`sam.FLAG_REVERSE`	`int`	`0x10`	This segment is on the reverse strand.
`sam.FLAG_MATE_REVERSE`	`int`	`0x20`	The mate segment is on the reverse strand.
`sam.FLAG_FIRST`	`int`	`0x40`	This is the first segment of the template.
`sam.FLAG_LAST`	`int`	`0x80`	This is the last segment of the template.
`sam.FLAG_SECONDARY`	`int`	`0x100`	This is a secondary alignment.
`sam.FLAG_QC_FAIL`	`int`	`0x200`	The read failed platform or vendor quality checks.
`sam.FLAG_DUPLICATE`	`int`	`0x400`	The read is a PCR or optical duplicate.
`sam.FLAG_SUPPLEMENTARY`	`int`	`0x800`	This is a supplementary alignment.
`sam.MISSING`	`string`	`"*"`	Placeholder used for an absent column.

Functions

function	description
`sam.open(path as string)`	Open a SAM file for streaming, capturing its header block.
`sam.openStdin()`	Open standard input as a SAM stream.
`sam.next(r as Reader)`	Advance the cursor to the next alignment record.
`sam.close(r as Reader)`	Close the cursor and release its decompressor.
`sam.closeStrict(r as Reader)`	Close a fully-consumed cursor, raising if its decompressor failed.
`sam.parse(line as string)`	Parse one SAM alignment line.
`sam.format(rec as Record)`	Render an alignment back to a SAM record line.
`sam.hasFlag(rec as Record, bit as int)`	Whether a FLAG bit is set on a record.
`sam.isUnmapped(rec as Record)`	Whether the record is unmapped.
`sam.isReverse(rec as Record)`	Whether the record is mapped to the reverse strand.
`sam.isSecondary(rec as Record)`	Whether the record is a secondary alignment.
`sam.isSupplementary(rec as Record)`	Whether the record is a supplementary alignment.
`sam.isDuplicate(rec as Record)`	Whether the record is flagged as a PCR or optical duplicate.
`sam.isPrimary(rec as Record)`	Whether the record is a primary alignment: mapped, not secondary, not supplementary.
`sam.strandOf(rec as Record)`	The strand a record aligns to.
`sam.parseCigar(cigar as string)`	Split a CIGAR string into its operations.
`sam.referenceLength(cigar as string)`	Number of reference bases a CIGAR string consumes.
`sam.queryLength(cigar as string)`	Number of query bases a CIGAR string consumes.
`sam.toInterval(rec as Record)`	The reference interval an alignment covers, as a half-open interval.
`sam.tagValue(rec as Record, tagName as string, fallback as string)`	Read the value of an optional tag.
`sam.referenceSizes(r as Reader)`	The reference sequences declared in the header, as chromosome sizes.
`sam.headerOf(path as string)`	Read just the `@` header block of a SAM file.

`vcf`

Streaming VCF reading and writing, INFO and per-sample FORMAT access.

Types

type	kind	description
`vcf.Variant`	struct	One VCF variant record.
`vcf.Reader`	struct	A streaming VCF cursor, carrying the file's header.
`vcf.Next`	enum	The result of advancing a VCF cursor.

Constants

constant	type	value	description
`vcf.MISSING`	`string`	`"."`	Placeholder used for an absent column.
`vcf.FIXED_COLUMNS`	`int`	`9`	Number of fixed columns before the per-sample genotype columns.

Functions

function	description
`vcf.open(path as string)`	Open a VCF file for streaming, capturing its header.
`vcf.openStdin()`	Open standard input as a VCF stream.
`vcf.next(r as Reader)`	Advance the cursor to the next variant record.
`vcf.close(r as Reader)`	Close the cursor and release its decompressor.
`vcf.closeStrict(r as Reader)`	Close a fully-consumed cursor, raising if its decompressor failed.
`vcf.headerOf(path as string)`	Read just the header lines of a VCF file.
`vcf.parse(line as string)`	Parse one VCF variant line.
`vcf.parseInfo(text as string)`	Parse a VCF INFO column into a map.
`vcf.info(v as Variant, key as string, fallback as string)`	Read an INFO field, or a fallback when it is absent.
`vcf.hasInfo(v as Variant, key as string)`	Whether an INFO flag is present.
`vcf.passed(v as Variant)`	Whether the variant passed every filter.
`vcf.isSnv(v as Variant)`	Whether the variant is a single-nucleotide substitution.
`vcf.isIndel(v as Variant)`	Whether the variant is an insertion or deletion.
`vcf.sampleValue(v as Variant, sampleIndex as int, key as string, fallback as string)`	The per-sample value of one FORMAT key.
`vcf.genotype(v as Variant, sampleIndex as int)`	The genotype call of one sample.
`vcf.toInterval(v as Variant)`	The reference span of a variant, as a half-open interval.
`vcf.format(v as Variant)`	Render a variant back to a VCF record line.
`vcf.formatInfo(entries as map of string to string)`	Render an INFO map back to its column text.

`intervals`

Interval arithmetic over genomic features - the bedtools-lite layer.

Types

type	kind	description
`intervals.Interval`	struct	A half-open genomic interval.

Constants

constant	type	value	description
`intervals.KEY_WIDTH`	`int`	`12`	Width used when zero-padding coordinates into sort keys.
`intervals.MAX_COORDINATE`	`int`	`1000000000000`	One past the largest coordinate an interval may carry.

Functions

function	description
`intervals.make(chrom as string, start as int, end as int)`	Build an unnamed, unstranded interval.
`intervals.named(chrom as string,

start as int, end as int, name as string, score as float, strand as string) | Build a fully specified interval. | | intervals.length(iv as Interval) | Width of an interval in bases. | | intervals.overlaps(a as Interval, b as Interval) | Whether two intervals share at least one base. | | intervals.overlapLength(a as Interval, b as Interval) | Number of bases two intervals share. | | intervals.contains(outer as Interval, inner as Interval) | Whether outer fully contains inner. | | intervals.intersection(a as Interval, b as Interval) | The shared region of two overlapping intervals. | | intervals.sortKey(iv as Interval) | Sort key for one interval: chromosome, then zero-padded start and end. | | intervals.sort(ivs as list of Interval) | Sort intervals by chromosome then start then end. | | intervals.merge(ivs as list of Interval, maxGap as int) | Merge overlapping and nearby intervals, per chromosome. | | intervals.totalLength(ivs as list of Interval) | Total number of bases covered, counting overlaps once. | | intervals.intersect(a as list of Interval, b as list of Interval) | Pairwise intersection regions between two interval sets. | | intervals.countOverlaps(a as list of Interval, b as list of Interval) | Count, for each query interval, how many target intervals it overlaps. | | intervals.coverage(a as list of Interval, b as list of Interval) | Bases of each query interval covered by the target set. | | intervals.subtract(a as list of Interval, b as list of Interval) | Remove from each query interval every base covered by the target set. | | intervals.complement(ivs as list of Interval, sizes as map of string to int) | The gaps between intervals, across whole chromosomes. | | intervals.slop(iv as Interval, left as int, right as int, limit as int) | Grow an interval on both sides, clamped at zero and an optional chromosome end. | | intervals.byChromosome(ivs as list of Interval) | Group intervals by chromosome. | | intervals.toBed3(iv as Interval)` | Render an interval as a three-column BED line. |

`qc`

One-pass streaming read QC - the FastQC-lite layer.

Types

type	kind	description
`qc.Options`	struct	How to run an analysis.
`qc.Report`	struct	Everything one pass measured.

Constants

constant	type	value	description
`qc.MAX_PHRED`	`int`	`94`	Highest Phred score tracked; covers the whole printable ASCII range.
`qc.Q30`	`int`	`30`	Quality score at or above which a base is counted towards Q30.
`qc.DEFAULT_BATCH`	`int`	`2000`	Records buffered before each batch of Go-speed counting.
`qc.DEFAULT_BATCH_BASES`	`int`	`4000000`	Bases buffered before a batch is counted, whichever limit is reached first.
`qc.ADAPTER_TRUSEQ`	`string`	`"AGATCGGAAGAGC"`	Illumina TruSeq / NEBNext universal adapter prefix.
`qc.ADAPTER_NEXTERA`	`string`	`"CTGTCTCTTATACACATCT"`	Nextera / Illumina transposase adapter prefix.
`qc.ADAPTER_SMALL_RNA`	`string`	`"TGGAATTCTCGG"`	Illumina small-RNA 3' adapter prefix.
`qc.ARTEFACT_POLY_G`	`string`	`"GGGGGGGGGG"`	Poly-G run, the two-colour-chemistry artefact seen on NovaSeq / NextSeq.

Functions

function	description
`qc.options()`	Default analysis options: every read, no per-position quality, Phred+33.
`qc.defaultAdapters()`	The adapters and artefacts counted when `Options.adapters` is empty.
`qc.analyze(path as string, opts as Options)`	Run a single streaming pass over a FASTQ file.
`qc.meanQuality(rep as Report)`	Mean Phred quality across every sampled base.
`qc.q30Percent(rep as Report)`	Percentage of sampled bases at Q30 or better.
`qc.gcPercent(rep as Report)`	G+C content of the sampled bases as a percentage.
`qc.meanLength(rep as Report)`	Mean sampled read length.
`qc.perBaseMean(rep as Report)`	Mean quality at each read position.
`qc.summary(rep as Report)`	Render a report as a human-readable text summary.

`trim`

Trimming, filtering and subsampling - the fastp-lite layer.

Types

type	kind	description
`trim.Options`	struct	How to trim and filter.
`trim.Stats`	struct	What a run did.

Constants

constant	type	value	description
`trim.DEFAULT_WINDOW`	`int`	`4`	Default sliding window width for quality trimming.
`trim.DEFAULT_OVERLAP`	`int`	`6`	Shortest partial adapter match accepted at a read's 3' end.

Functions

function	description
`trim.options()`	Default options: adapter clipping on, sliding-window quality trimming at Q20, and reads shorter than 25 bases discarded.
`trim.run(inPath as string, outPath as string, opts as Options)`	Stream a FASTQ file through trimming and filtering into a new file.
`trim.trimRead(rec as fastq.Read, opts as Options)`	Apply every configured trimming step to one record.
`trim.clipFixed(rec as fastq.Read, front as int, tail as int)`	Remove a fixed number of bases from each end.
`trim.clipAdapters(rec as fastq.Read, adapters as list of string, minOverlap as int)`	Clip the read at the first adapter occurrence, including a partial adapter running off the 3' end.
`trim.adapterStart(seq as string, adapters as list of string, minOverlap as int)`	The earliest position at which an adapter starts in a sequence.
`trim.clipQuality(rec as fastq.Read, threshold as int, window as int, offset as int)`	Trim the 3' end where a sliding window's mean quality falls below a threshold.
`trim.qualityKeepLength(qual as string, threshold as int, window as int, offset as int)`	How many bases survive sliding-window quality trimming.
`trim.truncate(rec as fastq.Read, maxLength as int)`	Cap a record's length, keeping the 5' end.
`trim.keeps(rec as fastq.Read, opts as Options)`	Whether a trimmed record passes the configured filters.
`trim.subsampleEvery(inPath as string, outPath as string, everyNth as int, maxReads as int)`	Copy every Nth record of a FASTQ file to a new file.
`trim.subsampleFraction(inPath as string, outPath as string, fraction as float)`	Copy a random fraction of a FASTQ file to a new file.

`pipeline`

Run, skip, check and fan out external tools.

Types

type	kind	description
`pipeline.Job`	struct	One step of a pipeline.
`pipeline.Result`	struct	What running a job produced.

Functions

function	description
`pipeline.job(name as string, argv as list of string)`	Build a job from a name and an argv.
`pipeline.shell(name as string, cmdline as string)`	Build a job that runs a shell command line.
`pipeline.needing(j as Job, inputs as list of string)`	A copy of the job that declares the files it reads.
`pipeline.producing(j as Job, outputs as list of string)`	A copy of the job that declares the files it produces.
`pipeline.feeding(j as Job, text as string)`	A copy of the job with text to feed to its standard input.
`pipeline.tolerant(j as Job)`	A copy of the job whose failure is reported but not fatal.
`pipeline.needsRun(j as Job)`	Whether a job still needs to run.
`pipeline.run(j as Job)`	Run one job, skipping it when its outputs are already up to date.
`pipeline.runAll(jobs as list of Job)`	Run jobs one after another, stopping at the first real failure.
`pipeline.runParallel(jobs as list of Job, width as int)`	Run jobs concurrently, at most `width` at a time.
`pipeline.check(res as Result)`	Raise when a result represents a real failure.
`pipeline.checkAll(results as list of Result)`	Raise on the first real failure in a batch of results.
`pipeline.allOk(results as list of Result)`	Whether every result succeeded or was tolerated.
`pipeline.hasTool(name as string)`	Whether an executable is on `PATH`.
`pipeline.requireTools(names as list of string)`	Raise unless every named tool is available.
`pipeline.workDir(tag as string)`	A scratch directory that the caller is responsible for removing.
`pipeline.cleanUp(dir as string)`	Remove a directory and everything under it.
`pipeline.summary(results as list of Result)`	Render results as one status line per job.

`ngs`

The deck entry module: identity and host capabilities.

Types

type	kind	description
`ngs.Capabilities`	struct	What this host can and cannot do with the deck.

Constants

constant	type	value	description
`ngs.VERSION`	`string`	`"0.1.0"`	The deck's version.
`ngs.NAME`	`string`	`"@jennifer/ngs"`	The deck's canonical package name.

Functions

function	description
`ngs.capabilities()`	What the current interpreter and host support.
`ngs.describe()`	A one-line description of the deck and what this host supports.
`ngs.requireFullHost()`	Raise unless the host can stream gzip and drive external tools.

244 exported names across 12 modules.

#Cheatsheet

#core

#Constants

#Functions

#source

#Types

#Constants

#Functions

#fastq

#Types

#Constants

#Functions

#bed

#Types

#Constants

#Functions

#gff

#Types

#Constants

#Functions

#sam

#Types

#Constants

#Functions

#vcf

#Types

#Constants

#Functions

#intervals

#Types

#Constants

#Functions

#qc

#Types

#Constants

#Functions

#trim

#Types

#Constants

#Functions

#pipeline

#Types

#Functions

#ngs

#Types

#Constants

#Functions

Cheatsheet

`core`

Constants

Functions

`source`

Types

Constants

Functions

`fastq`

Types

Constants

Functions

`bed`

Types

Constants

Functions

`gff`

Types

Constants

Functions

`sam`

Types

Constants

Functions

`vcf`

Types

Constants

Functions

`intervals`

Types

Constants

Functions

`qc`

Types

Constants

Functions

`trim`

Types

Constants

Functions

`pipeline`

Types

Functions

`ngs`

Types

Constants

Functions