Dev (#1)

Updated Readme.md; added Dockerfile

Author: EgorGuga

Dockerfile

@@ -0,0 +1,49 @@
+FROM phusion/baseimage:jammy-1.0.1
+
+ARG HTSLIB_VERSION=1.17
+
+ENV TERM=xterm-256color \
+    HTSLIB_URL=https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2
+
+COPY . minimap2_index_modifier
+
+# install deps and cleanup apt garbage
+RUN set -eux; \
+  apt-get update; \
+  apt-get install -y \
+    wget \
+    make \
+    autoconf \
+    gcc \
+    libcurl4-openssl-dev \
+    zlib1g-dev \
+    libbz2-dev \
+    liblzma-dev \
+    bzip2 \
+  && rm -rf /var/lib/apt/lists/*;
+
+#install htslib
+RUN set -eux; \
+mkdir temp; \
+cd temp; \
+\
+wget ${HTSLIB_URL}; \
+tar -xf htslib-${HTSLIB_VERSION}.tar.bz2; \
+cd htslib-${HTSLIB_VERSION}; \
+\
+autoreconf -i; \
+./configure; \
+make; \
+make install; \
+cd ../../; \
+rm -rf temp;
+
+#install minimap2_index_modifier
+RUN set -eux; \
+cd minimap2_index_modifier; \
+make; \
+cp minimap2 /usr/local/bin; \
+cd ../; \
+rm -rf minimap2_index_modifier;
+
+ENV LD_LIBRARY_PATH=/usr/local/lib

README.md

@@ -1,32 +1,47 @@
-## Build
-install htslib 1.17
-make
+Minimap2_index_modifier
+=======================
+Minimap2_index_modifier is a fork of alignment tool [minimap2](https://github.com/lh3/minimap2).
+Unlike the original tool, this can use the variants defined in the VCF file when generating the index, for more accurate alignment.
 
-## Make gz and gz.tbi from VCF
-bgzip -c filename.vcf > filename.vcf.gz\
-tabix -p vcf filename.vcf.gz
 
-## Run modified index creation
-bgzip -c test.vcf > test.vcf.gz\
-tabix -p vcf test.vcf.gz\
-./minimap2 -d test/test.modified.mni --vcf-file-with-variants test/test_long_chr1.vcf.gz test/test.fasta
+Minimap2_index_modifier can be used in the same way as the original minimap2.  
+To create a modified index use additional parameter `--vcf-file-with-variants <vcf-file>`.
+```bash
+minimap2 -d index.mmi --vcf-file-with-variants input.vcf.gz reference.fasta
+```
 
-Use flag --parse-haplotype if your VCF contains phased haplotypes
+Use flag `--parse-haplotype` if your VCF contains phased haplotypes.
 
-## Run test
+## Contents
+* [Installation](#installation)
+  * [Compiling from source](#compiling-from-source)
+  * [Docker](#docker)
+* [Pre-built indexes](#pre-built-indexes)
+* [Tests](#tests)
 
-### Empty test
-./minimap2 -d test/test.mni test/test.fasta\
-./minimap2 -d test/test.modified.mni --vcf-file-with-variants test/empty.vcf.gz test/test.fasta\
-diff test/test.mni test/test.modified.mni
+## Installation
+### Compiling from source
+To compile from source, use this version of tools:
 
+* GCC/G++ 11.4.0+
+* HTSlib v1.17
 
-### The same test
-./minimap2 -d test/test.mni test/test.fasta\
-./minimap2 -d test/test.modified.mni --vcf-file-with-variants test/test_long_chr1_the_same.vcf.gz test/test.fasta\
-diff test/test.mni test/test.modified.mni
+Command to compile:
+```bash
+cd minimap2_index_modifier && make
+```
+
+### Docker
+Clone this repository and build a Docker image as follows.
+```bash
+docker build -t minimap2_index_modifier:2.24 .
+```
+
+## Pre-built indexes
+This [link](https://nextcloud.ispras.ru/index.php/s/wcb9PpZyr8Gb5CC) contains pre-built modified indexes for next references:
+* GRCh38 [(GCA_000001405.15)](https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/references/GRCh38/)
+* GRCh37 [(hs37d5)](https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/references/GRCh37/)
+
+## Tests
+See [test/tests.md](test/tests.md) for more details.
 
-### Not the same test
-./minimap2 -d test/test.mni test/test.fasta\
-./minimap2 -d test/test.modified.mni --vcf-file-with-variants test/test_long_chr1_not_the_same.vcf.gz test/test.fasta\
-diff test/test.mni test/test.modified.mni

test/README.md

@@ -0,0 +1,32 @@
+## Tests for minimap2_index_modiifer
+There are three tests to check base functionality.
+
+### Common test
+This test create two index files: regular and modified.
+```bash
+minimap2 -d test/test.mni test/test.fasta
+minimap2 -d test/test.modified.mni --vcf-file-with-variants test/test_long_chr1_not_the_same.vcf.gz test/test.fasta
+diff test/test.mni test/test.modified.mni
+```
+
+Modified index file should contains extra string and some strings should be mismatched.
+
+### Empty VCF test
+If input VCF file contains no variants from reference modified index would be same as regular one.
+```bash
+minimap2 -d test/test.mni test/test.fasta
+minimap2 -d test/test.modified.mni --vcf-file-with-variants test/empty.vcf.gz test/test.fasta
+diff test/test.mni test/test.modified.mni
+```
+
+Index files should be the same (empty output after third command).
+
+### Pseudo-variants test
+In this test `test/test_long_chr1_the_same.vcf.gz` contains pseudo-variants (like A -> A, C -> C, etc). This variants would be processed with no effect.
+```bash
+minimap2 -d test/test.mni test/test.fasta
+minimap2 -d test/test.modified.mni --vcf-file-with-variants test/test_long_chr1_the_same.vcf.gz test/test.fasta
+diff test/test.mni test/test.modified.mni
+```
+
+Index files should be the same.