<commit_before>#!/usr/bin/env bash
set -ex

FASTA=../data/human_g1k_v37.fa.gz
FASTQ_PREFIX=HG0019-mq0
BAM=../alignment-accuracy/HG00119-bwa.bam
OUTBAM=HG0019-mq0.bam 

mitty -v4 debug bam-to-truth ${BAM} 0 HG00019 ${FASTQ_PREFIX}
 
bwa mem ${FASTA} ${FASTQ_PREFIX}-1.fq ${FASTQ_PREFIX}-2.fq | samtools view -bSho temp0.bam<commit_msg>Update bam_to_truth.sh<commit_after>#!/usr/bin/env bash
set -ex

FASTA=../data/human_g1k_v37.fa.gz
FASTQ_PREFIX=HG0019-mq0
BAM=../alignment-accuracy/HG00119-bwa.bam

mitty -v4 debug bam-to-truth ${BAM} 0 HG00019 ${FASTQ_PREFIX}
 
bwa mem ${FASTA} ${FASTQ_PREFIX}-1.fq ${FASTQ_PREFIX}-2.fq | samtools view -bSho temp0.bam
{'fraction_non_alphanumeric': 0.1620795107033639, 'fraction_numerical': 0.0779816513761468, 'mean_word_length': 4.598290598290598, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, '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': '3074121', 'n_tokens_mistral': 358, 'n_tokens_neox': 307, 'n_words': 49}