hts-nim

v0.2.23 of hts-nim will be the last version that supports htslib below 1.10 (which was release in early december 2019). The master branch requires htslib 1.10 and higher and will be backward incompatible with previous releases.

This is a wrapper for htslib in nim.

Nim is a fast, garbage-collected language that compiles to C and has a syntax that's not too different to python.

If you use this library, please cite the paper

Projects using hts-nim are accumulating in the wiki

Installation

See Section Below

Usage

Examples of hts-nim tools are available in the hts-nim-tools repo

below are examples of the syntax in this library see the docs for more info:

Also see examples and other repos using hts-nim in the wiki

BAM / CRAM / SAM

See API docs here

```nim import hts

open a bam/cram and look for the index.

var b:Bam open(b, "tests/HG02002.bam", index=true, fai="/data/human/g1kv37decoy.fa")

for record in b: if record.mapping_quality > 10u: echo record.chrom, record.start, record.stop

regional queries:

for record in b.query("6", 30816675, 32816675): if record.flag.proper_pair and record.flag.reverse: # cigar is an iterable of operations: for op in record.cigar: # $op gives the string repr of the operation, e.g. '151M' echo $op, " ", op.consumes.reference, " ", op.consumes.query

# tags are pulled by type `ta`
var mismatches = tag[int](record, "NM")
if not mismatches.isNone and mismatches.get < 3:
  var rg = tag[string](record, "RG")
  if not rg.isNone: echo rg.get

```

VCF / BCF

See API docs here

```nim import hts

var tsamples = @["101976-101976", "100920-100920", "100231-100231", "100232-100232", "100919-100919"]

VCF and BCF supported

var v:VCF doAssert(open(v, "tests/test.bcf", samples=tsamples))

var afs = newseqfloat32 # size doesn't matter. this will be re-sized as needed var acs = newseqint32 # size doesn't matter. this will be re-sized as needed var csq = newstringofcap(20) for rec in v: echo rec, " qual:", rec.QUAL, " filter:", rec.FILTER var info = rec.info # accessing stuff from the INFO field is meant to be as fast as possible, allowing # the user to re-use memory as needed. doAssert info.get("CSQ", csq) == Status.OK # string doAssert info.get("AC", acs) == Status.OK # ints doAssert info.get("AF", afs) == Status.OK # floats echo acs, afs, csq, info.hasflag("IN_EXAC")

# accessing format fields is similar var dps = new_seqint32 doAssert rec.format.get("DP", dps) == Status.OK

open a VCF for writing

var wtr:VCF doAssert(open(wtr, "tests/outv.vcf", mode="w")) wtr.header = v.header doAssert(wtr.write_header())

regional queries look for index. works for VCF and BCF

for rec in v.query("1:15600-18250"): echo rec.CHROM, ":", $rec.POS # adjust some values in the INFO var val = 22.3 doAssert rec.info.set("VQSLOD", val) == Status.OK doAssert wtr.write_variant(rec)

Generate index files - .vcf.gz (tbi + csi ) & .bcf (csi)

var fnameInNew = "tests/test.bcf" var fnameIndexCsi = "tests/test00.bcf.csi" bcfBuildIndex(fnameInNew, fnameIndexCsi, true) # true for csi and false for tbi

```

TSV files

```nim import hts

var b: BGZI doAssert b.open("ti.txt.gz") # Requires a CSI index: ti.txt.gz.csi

for reg in b.query("aaa", 1, 5): echo reg ```

Setup / Installation

hts-nim requires that htslib is installed and the shared library is available (use LD_LIBRARY_PATH if it is not in a standard location).

If you use docker, you can use one of these images to get Nim installed.

Or you can copy the Dockerfile from this repo

If you don't use docker, you can use choosenim to quickly install Nim and nimble.

Users can also either follow or run scripts/simple-install.sh which sets up Nim and nimble ready for use and shows the needed adjustments to $PATH.

Once Nim is set up, hts-nim can be installed with nimble install -y from the root of this repository.

In all cases, it's recommended to use nim version 0.18.0 or more recent.

Then, from this repo you can run nimble test and nimble install and then you can save the above snippets into some.nim and run them with nim c -d:release -r some.nim. This will run them and save an executable named some.

Static Builds

hts-nim is meant to simplify and speed development and distribution. To that end, there is some machinery to help create truly static binaries for linux from nim-projects and for simple nim scripts. This means that there is no dependency on libhts.so. These builds only require docker and this static binary.

For a single file application that does not have a nimble file we can specify the dependencies using --deps:

hts_nim_static_builder -s vcf_cleaner.nim --deps "hts@>=0.2.7" --deps "binaryheap"

This will create a static binary at ./vcf_cleaner.

Projects with .nimble files can use that directly to indicate dependencies. For example, to build slivar, we can do:

hts_nim_static_builder -s ../slivar/src/slivar.nim -n ../slivar/slivar.nimble

After this finishes, a static slivar binary will appear in the current working directory.

We can verify that it is static using:

$ file ./slivar ./slivar: ELF 64-bit LSB executable, x86-64, version 1 (GNU/Linux), statically linked, for GNU/Linux 2.6.18, BuildID[sha1]=c2b5b52cb7be7f81bf90355a4e44a08a08df91d8, not stripped

The docker image is based on alpine linux and uses musl to create truly static binaries. At this time, libcurl is not supported so only binaries built using this method will only be able to access local files (no http/https/s3/gcs).

The docker images does use libdeflate by default. That provides, for example, a 20% speed improvement when used to build mosdepth.

Static binary with singularity

The default static build setup uses docker on linux. This is not possible on some clusters. To build a project using singularity, use something like this:

singularity run \ --bind $(pwd):/load \ --bind /scratch \ --bind /uufs \ 'docker://brentp/musl-hts-nim:latest' /usr/local/bin/nsb -n slivar.nimble -s src/slivar.nim -- -d:danger -d:release where the first bind is required as-is. The other binds can be modified to adjust which paths on the machine need to be available to access all local source files. This command will create a slivar executable in pwd. Then, replace slivar.nimble with your nimble file and src/slivar.nim with your main source file. It's also sometimes useful to replace -d:danger -d:release with -d:debug to get a debug build.