<commit_before>#include <cstdlib>
#include <stdexcept>
#include "json2pb.h"
#include "pileup_augmenter.hpp"
#include "stream.hpp"

using namespace std;

namespace vg {

const double PileupAugmenter::Log_zero = (double)-1e100;

const char PileupAugmenter::Default_default_quality = 30;
const int PileupAugmenter::Default_min_aug_support = 1;

PileupAugmenter::PileupAugmenter(VG* graph,
               int default_quality,
               int min_aug_support):
    _graph(graph),
    _default_quality(default_quality),
    _min_aug_support(min_aug_support) {
    assert(_min_aug_support > 0);
    _max_id = _graph->max_node_id();
    _node_divider._max_id = &_max_id;
    _augmented_graph.base_graph = graph;
}

// delete contents of table
PileupAugmenter::~PileupAugmenter() {
    clear();
}

void PileupAugmenter::clear() {
    _node_calls.clear();<commit_msg>Don't lower augmentation threshold in pileup mode<commit_after>#include <cstdlib>
#include <stdexcept>
#include "json2pb.h"
#include "pileup_augmenter.hpp"
#include "stream.hpp"

using namespace std;

namespace vg {

const double PileupAugmenter::Log_zero = (double)-1e100;

const char PileupAugmenter::Default_default_quality = 30;
const int PileupAugmenter::Default_min_aug_support = 2;

PileupAugmenter::PileupAugmenter(VG* graph,
               int default_quality,
               int min_aug_support):
    _graph(graph),
    _default_quality(default_quality),
    _min_aug_support(min_aug_support) {
    assert(_min_aug_support > 0);
    _max_id = _graph->max_node_id();
    _node_divider._max_id = &_max_id;
    _augmented_graph.base_graph = graph;
}

// delete contents of table
PileupAugmenter::~PileupAugmenter() {
    clear();
}

void PileupAugmenter::clear() {
    _node_calls.clear();
{'fraction_non_alphanumeric': 0.10763097949886105, 'fraction_numerical': 0.010250569476082005, 'mean_word_length': 4.760655737704918, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 11, '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': '7116462', 'n_tokens_mistral': 649, 'n_tokens_neox': 632, 'n_words': 111}