<commit_before>#!/bin/bash

NUM_THREADS=4
MAX_OVERLAP=90

for R1 in $(ls *_trim_1P.gz)
do
  R2=${R1/_1P/_2P}
  OUT_NAME=${R1/_trim_1P.gz/}
  echo $R1 $R2 $OUT_NAME
  flash $R1 $R2 -o $OUT_NAME -t $NUM_THREADS -M $MAX_OVERLAP --interleaved-output
done

<commit_msg>take the sample name to run FLASH<commit_after>#!/bin/bash

NUM_THREADS=4
MAX_OVERLAP=90

SAMPLE=$!

for R1 in $(ls *$SAMPLE*_trim_1P.gz)
do
  R2=${R1/_1P/_2P}
  OUT_NAME=${R1/_trim_1P.gz/}
  echo $R1 $R2 $OUT_NAME
  flash $R1 $R2 -o $OUT_NAME -t $NUM_THREADS -M $MAX_OVERLAP --interleaved-output
done


{'fraction_non_alphanumeric': 0.15343915343915343, 'fraction_numerical': 0.05291005291005291, 'mean_word_length': 4.117117117117117, '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': '6577886', 'n_tokens_mistral': 292, 'n_tokens_neox': 279, 'n_words': 59}