--- a
+++ b/softwares_config/htseq_2.0.1.config
@@ -0,0 +1,140 @@
+usage: htseq-count [-h] [--version] [-f {sam,bam,auto}] [-r {pos,name}]
+                   [--max-reads-in-buffer MAX_BUFFER_SIZE]
+                   [-s {yes,no,reverse}] [-a MINAQUAL] [-t FEATURE_TYPE]
+                   [-i IDATTR] [--additional-attr ADDITIONAL_ATTRIBUTES]
+                   [--add-chromosome-info]
+                   [-m {union,intersection-strict,intersection-nonempty}]
+                   [--nonunique {none,all,fraction,random}]
+                   [--secondary-alignments {score,ignore}]
+                   [--supplementary-alignments {score,ignore}] [-o SAMOUTS]
+                   [-p {SAM,BAM,sam,bam}] [-d OUTPUT_DELIMITER]
+                   [-c OUTPUT_FILENAME] [--counts-output-sparse]
+                   [--append-output] [-n NPROCESSES]
+                   [--feature-query FEATURE_QUERY] [-q] [--with-header]
+                   samfilenames [samfilenames ...] featuresfilename
+
+This script takes one or more alignment files in SAM/BAM format and a feature
+file in GFF format and calculates for each feature the number of reads mapping
+to it. See http://htseq.readthedocs.io/en/master/count.html for details.
+
+positional arguments:
+  samfilenames          Path to the SAM/BAM files containing the mapped reads.
+                        If '-' is selected, read from standard input
+  featuresfilename      Path to the GTF file containing the features
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --version             Show software version and exit
+  -f {sam,bam,auto}, --format {sam,bam,auto}
+                        Type of <alignment_file> data. DEPRECATED: file format
+                        is detected automatically. This option is ignored.
+  -r {pos,name}, --order {pos,name}
+                        'pos' or 'name'. Sorting order of <alignment_file>
+                        (default: name). Paired-end sequencing data must be
+                        sorted either by position or by read name, and the
+                        sorting order must be specified. Ignored for single-
+                        end data.
+  --max-reads-in-buffer MAX_BUFFER_SIZE
+                        When <alignment_file> is paired end sorted by
+                        position, allow only so many reads to stay in memory
+                        until the mates are found (raising this number will
+                        use more memory). Has no effect for single end or
+                        paired end sorted by name
+  -s {yes,no,reverse}, --stranded {yes,no,reverse}
+                        Whether the data is from a strand-specific assay.
+                        Specify 'yes', 'no', or 'reverse' (default: yes).
+                        'reverse' means 'yes' with reversed strand
+                        interpretation
+  -a MINAQUAL, --minaqual MINAQUAL
+                        Skip all reads with MAPQ alignment quality lower than
+                        the given minimum value (default: 10). MAPQ is the 5th
+                        column of a SAM/BAM file and its usage depends on the
+                        software used to map the reads.
+  -t FEATURE_TYPE, --type FEATURE_TYPE
+                        Feature type (3rd column in GTF file) to be used, all
+                        features of other type are ignored (default, suitable
+                        for Ensembl GTF files: exon)
+  -i IDATTR, --idattr IDATTR
+                        GTF attribute to be used as feature ID (default,
+                        suitable for Ensembl GTF files: gene_id). All feature
+                        of the right type (see -t option) within the same GTF
+                        attribute will be added together. The typical way of
+                        using this option is to count all exonic reads from
+                        each gene and add the exons but other uses are
+                        possible as well. You can call this option multiple
+                        times: in that case, the combination of all attributes
+                        separated by colons (:) will be used as a unique
+                        identifier, e.g. for exons you might use -i gene_id -i
+                        exon_number.
+  --additional-attr ADDITIONAL_ATTRIBUTES
+                        Additional feature attributes (default: none, suitable
+                        for Ensembl GTF files: gene_name). Use multiple times
+                        for more than one additional attribute. These
+                        attributes are only used as annotations in the output,
+                        while the determination of how the counts are added
+                        together is done based on option -i.
+  --add-chromosome-info
+                        Store information about the chromosome of each feature
+                        as an additional attribute (e.g. colunm in the TSV
+                        output file).
+  -m {union,intersection-strict,intersection-nonempty}, --mode {union,intersection-strict,intersection-nonempty}
+                        Mode to handle reads overlapping more than one feature
+                        (choices: union, intersection-strict, intersection-
+                        nonempty; default: union)
+  --nonunique {none,all,fraction,random}
+                        Whether and how to score reads that are not uniquely
+                        aligned or ambiguously assigned to features (choices:
+                        none, all, fraction, random; default: none)
+  --secondary-alignments {score,ignore}
+                        Whether to score secondary alignments (0x100 flag)
+  --supplementary-alignments {score,ignore}
+                        Whether to score supplementary alignments (0x800 flag)
+  -o SAMOUTS, --samout SAMOUTS
+                        Write out all SAM alignment records into SAM/BAM files
+                        (one per input file needed), annotating each line with
+                        its feature assignment (as an optional field with tag
+                        'XF'). See the -p option to use BAM instead of SAM.
+  -p {SAM,BAM,sam,bam}, --samout-format {SAM,BAM,sam,bam}
+                        Format to use with the --samout option.
+  -d OUTPUT_DELIMITER, --delimiter OUTPUT_DELIMITER
+                        Column delimiter in output (default: TAB).
+  -c OUTPUT_FILENAME, --counts_output OUTPUT_FILENAME
+                        Filename to output the counts to instead of stdout.
+  --counts-output-sparse
+                        Store the counts as a sparse matrix (mtx, h5ad, loom).
+  --append-output       Append counts output to an existing file instead of
+                        creating a new one. This option is useful if you have
+                        already creates a TSV/CSV/similar file with a header
+                        for your samples (with additional columns for the
+                        feature name and any additionl attributes) and want to
+                        fill in the rest of the file.
+  -n NPROCESSES, --nprocesses NPROCESSES
+                        Number of parallel CPU processes to use (default: 1).
+                        This option is useful to process several input files
+                        at once. Each file will use only 1 CPU. It is
+                        possible, of course, to split a very large input
+                        SAM/BAM files into smaller chunks upstream to make use
+                        of this option.
+  --feature-query FEATURE_QUERY
+                        Restrict to features descibed in this expression.
+                        Currently supports a single kind of expression:
+                        attribute == "one attr" to restrict the GFF to a
+                        single gene or transcript, e.g. --feature-query
+                        'gene_name == "ACTB"' - notice the single quotes
+                        around the argument of this option and the double
+                        quotes around the gene name. Broader queries might
+                        become available in the future.
+  -q, --quiet           Suppress progress report
+  --with-header         Whether to add a column header to the output TSV file
+                        indicating which column corresponds to which input BAM
+                        file. Only used if output to console or tsv or csv
+                        file. Default to False.
+
+Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology
+Laboratory (EMBL), Givanna Putri (g.putri@unsw.edu.au) and Fabio Zanini
+(fabio.zanini@unsw.edu.au), UNSW Sydney. (c) 2010-2021. Released under the
+terms of the GNU General Public License v3. Please cite the following paper if
+you use this script: G. Putri et al. Analysing high-throughput sequencing data
+in Python with HTSeq 2.0. Bioinformatics (2022).
+https://doi.org/10.1093/bioinformatics/btac166. Part of the 'HTSeq' framework,
+version 2.0.1.