<commit_before># rseqc Infer Experiment

[website](http://rseqc.sourceforge.net/#infer-experiment-py)

## Examples

Minimal usage:

```python
rule infer_experiment:
    input: bam = 'a.bam',
           bed = 'b.bed'
    output: 'b.txt'
    log: 'a.infer_experiment.log'
    wrapper:
        'file://path/to/wrapper'
```

## Input

`bam`:
    Input alignment file in BAM format.

`bed`:
    Reference gene model in bed format.

## Output

Output files are simply copies of input.

### Single-end mode:

Expects a single unnamed output file

## Threads
Does not use threads

## Params
`extra`:
    Command line parameters that will be passed directly to rseqc infer_exerpiment.py

    Possible command include::

        -s SAMPLE_SIZE, --sample-size=SAMPLE_SIZE
            Number of reads sampled from BAM [200000].
        -q MAP_QUAL, --mapq=MAP_QUAL
            Minimum mapping quality (phred scaled) for an alignment to be considered [30].
<commit_msg>Updates bam_stat readme.<commit_after># rseqc Infer Experiment

[website](http://rseqc.sourceforge.net/#bam-stat-py)

## Examples

### Minimal usage:

```python
rule bam_stat:
    input: 
        bam = 'sample1.bam'
    output: 
        txt='sample1.bam_stat.txt'
    wrapper:
        'file://path/to/wrapper'
```

### Extra Arguments:

```python
rule bam_stat:
    input: 
        bam = 'sample1.bam'
    output: 
        txt='sample1.bam_stat.txt'
    params:
        extra='-q 20'
    wrapper:
        'file://path/to/wrapper'
```

## Input

`bam`:
    Input alignment file in BAM format.

## Output

`txt`: 
    Text file containing basic stats.

## Threads
Does not use threads

## Params
`extra`:
    Command line parameters that will be passed directly to rseqc bam_stat.py.
    See website for possible options.

## Log
Cannot use log, bam_stat.py writes output to STDERR which is captured in the output.txt option.
{'fraction_non_alphanumeric': 0.11389036721660457, 'fraction_numerical': 0.007450771687067589, 'mean_word_length': 2.805668016194332, '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': '7639440', 'n_tokens_mistral': 658, 'n_tokens_neox': 614, 'n_words': 189}