<commit_before>#!/usr/bin/env bash
export TMPDIR=/home/jacob/fake_mnt
python germ.py \
$TMPDIR/jstore \
--config "config.txt" \
--reference "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz" \
--phase "ftp://gsapubftp-anonymous@ftp.<EMAIL>institute.org/bundle/2.8/b37/1000G_phase1.indels.b37.vcf.gz" \
--mills "ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz" \
--dbsnp "ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/2.8/b37/dbsnp_138.b37.vcf.gz" \
--hapmap "ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/2.8/b37/hapmap_3.3.b37.vcf.gz" \
--omni "ftp://gsapubftp-anonymous@ftp.<EMAIL>.org/bundle/2.8/b37/1000G_omni2.5.b37.vcf.gz" \
--output_dir '/home/jacob/' \<commit_msg>Updated URLs in germline launch script<commit_after>#!/usr/bin/env bash
export TMPDIR=./fake_mnt
python germ.py \
$TMPDIR/jstore \
--config "config.txt" \
--reference "https://s3-us-west-2.amazonaws.com/cgl-pipeline-inputs/germline/hs37d5.fa" \
--phase "https://s3-us-west-2.amazonaws.com/cgl-pipeline-inputs/germline/1000G_phase1.indels.b37.vcf" \
--mills "https://s3-us-west-2.amazonaws.com/cgl-pipeline-inputs/germline/Mills_and_1000G_gold_standard.indels.b37.vcf" \
--dbsnp "https://s3-us-west-2.amazonaws.com/cgl-pipeline-inputs/germline/dbsnp_138.b37.vcf" \
--hapmap "https://s3-us-west-2.amazonaws.com/cgl-pipeline-inputs/germline/hapmap_3.3.b37.vcf" \
--omni "https://s3-us-west-2.amazonaws.com/cgl-pipeline-inputs/germline/1000G_omni2.5.b37.vcf" \
-o '/home/jacob/' \
{'fraction_non_alphanumeric': 0.19535175879396985, 'fraction_numerical': 0.06532663316582915, 'mean_word_length': 4.073248407643312, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 6, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 3, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2733777', 'n_tokens_mistral': 780, 'n_tokens_neox': 722, 'n_words': 51}