1samtools-quickcheck(1)       Bioinformatics tools       samtools-quickcheck(1)
2
3
4

NAME

6       samtools quickcheck - a rapid sanity check on input files
7

SYNOPSIS

9       samtools quickcheck [options] in.sam|in.bam|in.cram [ ... ]
10
11

DESCRIPTION

13       Quickly  check that input files appear to be intact. Checks that begin‐
14       ning of the file contains a valid header (all  formats)  containing  at
15       least  one  target  sequence  and then seeks to the end of the file and
16       checks that an end-of-file (EOF) is present and intact  (BAM  and  CRAM
17       only).
18
19       Data  in  the  middle  of the file is not read since that would be much
20       more time consuming, so please note that this command will  not  detect
21       internal corruption, but is useful for testing that files are not trun‐
22       cated before performing more intensive tasks on them.
23
24       This command will exit with a non-zero exit code  if  any  input  files
25       don't  have  a  valid  header or are missing an EOF block. Otherwise it
26       will exit successfully (with a zero exit code).
27
28

OPTIONS

30       -v      Verbose output: will additionally print the names of all  input
31               files  that don't pass the check to stdout. Multiple -v options
32               will cause additional messages regarding check  results  to  be
33               printed to stderr.
34
35       -q      Quiet  mode:  disables  warning  messages on stderr about files
36               that fail.  If both -q and -v options are used then the  appro‐
37               priate level of -v takes precedence.
38
39       -u      Expect  unmapped  input  data, so do not require targets in the
40               header.
41
42

AUTHOR

44       Written by Josh Randall from the Sanger Institute.
45
46

SEE ALSO

48       samtools(1)
49
50       Samtools website: <http://www.htslib.org/>
51
52
53
54samtools-1.13                     7 July 2021           samtools-quickcheck(1)