<commit_before>#!/bin/bash

set -xe

if [[ -z "${TMPDIR}" ]]; then
  TMPDIR=/tmp
fi

set -u

### alleleCount
VER_ALLELECOUNT="v4.0.0"

### cgpNgsQc
VER_CGPNGSQC="v1.5.1"
BIN_VERIFYBAMID='https://github.com/statgen/verifyBamID/releases/download/v1.1.3/verifyBamID'

### ascatNgs
VER_ASCATNGS="v4.2.0"
SRC_ASCAT="https://raw.githubusercontent.com/Crick-CancerGenomics/ascat/v2.5.1/ASCAT/R/ascat.R"

### grass
VER_GRASS="v2.1.0"

### BRASS
VER_BRASS="v6.1.1"
SOURCE_BLAT="http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip"
SRC_FASTA36="https://github.com/wrpearson/fasta36/archive/fasta-v36.3.8g.tar.gz"
<commit_msg>Update versions for tabix query issues on GRCh38<commit_after>#!/bin/bash

set -xe

if [[ -z "${TMPDIR}" ]]; then
  TMPDIR=/tmp
fi

set -u

### alleleCount
VER_ALLELECOUNT="v4.0.0"

### cgpNgsQc
VER_CGPNGSQC="v1.5.1"
BIN_VERIFYBAMID='https://github.com/statgen/verifyBamID/releases/download/v1.1.3/verifyBamID'

### ascatNgs
VER_ASCATNGS="v4.2.1"
SRC_ASCAT="https://raw.githubusercontent.com/Crick-CancerGenomics/ascat/v2.5.1/ASCAT/R/ascat.R"

### grass
VER_GRASS="v2.1.1"

### BRASS
VER_BRASS="v6.1.2"
SOURCE_BLAT="http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip"
SRC_FASTA36="https://github.com/wrpearson/fasta36/archive/fasta-v36.3.8g.tar.gz"

{'fraction_non_alphanumeric': 0.19825535289452814, 'fraction_numerical': 0.05075337034099921, 'mean_word_length': 4.842592592592593, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 6, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3347801', 'n_tokens_mistral': 638, 'n_tokens_neox': 608, 'n_words': 57}