htsfile(1)

1htsfile(1)                   Bioinformatics tools                   htsfile(1)
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NAME

6       htsfile - identify high-throughput sequencing data files
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SYNOPSIS

9       htsfile [-chHv] FILE...
10       htsfile --copy [-v] FILE DESTFILE
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DESCRIPTION

13       The  htsfile  utility attempts to identify what kind of high-throughput
14       sequencing data files the specified files  are,  and  provides  minimal
15       viewing capabilities for some kinds of data file.
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17       It can identify sequencing data files such as SAM, BAM, and CRAM; vari‐
18       ant calling data files such as VCF and BCF; index files used  to  index
19       these data files; and compressed versions of many of them.
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21       For  each  FILE  given, htsfile prints a description of the file format
22       determined, using similar keyword conventions to file(1): "text"  indi‐
23       cates  a textual file that can probably be viewed on a terminal; "data"
24       indicates binary data; "sequence", "variant calling", and "index" indi‐
25       cate different categories of data file.  When it can be identified, the
26       name of the particular file format (such as "BAM" or "VCF") is  printed
27       at the start of the description.
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29       When  used  to  view file contents as text, htsfile can optionally show
30       only headers or only data records, but has no other filtering capabili‐
31       ties.   Use  samtools or bcftools if you need more extensive viewing or
32       filtering capabilities.
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34       Alternatively, when --copy is used, htsfile takes exactly two arguments
35       and performs a byte-for-byte copy from FILE to DESTFILE.  This is simi‐
36       lar to cp(1), but HTSlib's remote file access facilities are  available
37       for both source and destination.
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39       The following options are accepted:
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41       -c, --view
42           Instead  of identifying the specified files, display a textual rep‐
43           resentation of their contents on standard output.
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45           By default, --view refuses to display  files  in  unknown  formats.
46           When  --verbose  is  also given, the raw contents of such files are
47           displayed, with non-printable characters  shown  via  C-style  "\x"
48           hexadecimal escape sequences.
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50       -C, --copy
51           Instead  of identifying or displaying the specified files, copy the
52           source FILE to the destination DESTFILE.   Only  --verbose  may  be
53           used in conjunction with --copy.
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55       -h, --header-only
56           Display data file headers only.  Implies --view.
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58       -H, --no-header
59           When viewing files, display data records only.
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61       -v, --verbose
62           Display  additional warnings and diagnostic messages.  Using --ver‐
63           bose repeatedly further raises the verbosity.
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NAME

SYNOPSIS

DESCRIPTION

SEE ALSO