## Install

### Dependencies

For building required HTSlib:
```
sudo apt install cmake libclang-dev

```

### Windows build

Install the native dependencies with Rtools/MSYS2:

```powershell
pacman -S --needed mingw-w64-x86_64-curl mingw-w64-x86_64-sqlite3 mingw-w64-x86_64-openssl mingw-w64-x86_64-tre mingw-w64-x86_64-libiconv mingw-w64-x86_64-gettext
```

Make sure these user environment variables are set:

```powershell
[Environment]::SetEnvironmentVariable("LIBCLANG_PATH", "$env:USERPROFILE\tools\libclang-win", "User")
[Environment]::SetEnvironmentVariable("PKG_CONFIG", "C:\rtools45\usr\bin\pkg-config.exe", "User")
[Environment]::SetEnvironmentVariable("PKG_CONFIG_PATH", "C:\rtools45\mingw64\lib\pkgconfig", "User")
```

Also ensure the user `Path` contains:

```text
%USERPROFILE%\tools\libclang-win
C:\rtools45\mingw64\bin
C:\rtools45\usr\bin
```

Then open a fresh PowerShell in the repository and run:

```powershell
.\setup-patches.ps1
cargo build
```

`setup-patches.ps1` generates the Windows-only local Cargo patch config in
`.cargo/config.toml` and patched crate sources in `patches/`. Both are ignored
by git. This keeps Linux builds on the registry crates while Windows builds use
the patched `hts-sys` / `rust-htslib` sources.

* minimap2 
* (samtools)[https://www.htslib.org/download/]
* (dorado)[https://github.com/nanoporetech/dorado]
* (bcftools)[https://www.htslib.org/download/]
* (modkit)[https://github.com/nanoporetech/modkit]
* VEP: cf pandora_lib_variants for VEP install
* nanomonsv (cf dependencies at github, TODO: use racon)

## Usage

### SomaticPipe output container

A proposed single-file container for SomaticPipe results is documented in
[`docs/somaticpipe-output-format.md`](docs/somaticpipe-output-format.md).

### Use jq for selecting variants

* Somatic Variants of chrM (25) 
```
zcat /data/longreads_basic_pipe/*/diag/somatic_variants.json.gz | \
jq -L ./jq_filters -C 'include "jq_variants"; [.data[] | select(contig("chrM") and n_in_constit <= 1) | format]'
```

### Using jq and find to look for chrM norm coverage
```
find /data/longreads_basic_pipe/ -name "*_diag_hs1_info.json" -type f -exec sh -c 'basename $(dirname $(dirname "{}")) | tr -d "\n"' \; -printf "\t" -exec jq -L ./jq_filters -r 'include "jq_bam"; contig_coverage("chrM")' {} \;
```

### Using jq and find VEP consequences (cf https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html)

```
zcat /data/longreads_basic_pipe/ADJAGBA/diag/somatic_variants.json.gz | jq -L ./jq_filters -C 'include "jq_variants"; consequence("SynonymousVariant")' | bat
```

### Using jq and find to count VEP consequences 
```
find /data/longreads_basic_pipe/ -name "somatic_variants.json.gz" -type f -exec sh -c 'dirname=$(basename $(dirname $(dirname "$1"))); count=$(zcat "$1" | jq -L ./jq_filters -r '\''include "jq_variants"; count_consequence("SynonymousVariant") | [.true_count, .total_count, .proportion] | @tsv'\''); echo "${dirname}\t${count}"' sh {} \;
```

### Find recurrence by VEP consequence
```
find /data/longreads_basic_pipe/ -name "somatic_variants.json.gz" -type f -exec sh -c 'dirname=$(basename $(dirname $(dirname "$1"))); count=$(zcat "$1" | jq -L ./jq_filters -r '\''include "jq_variants"; consequence("StopGained") | .[] | select(.has_consequence == true) | [.chr, .position, .ref, .alt] | @tsv'\''); echo "${count}"' sh {} \; | sort -k1,1V -k2,2n | uniq -c |  awk '$1 > 1 {print $2"\t"$3"\t"$4"\t"$5"\t"$1}'
```

### Reading log files
```
zcat /data/longreads_basic_pipe/ID/log/deepsomatic/deepvariant_e7ed1.log.gz | jq -r '.log'

```