Update README.md (#43)

Author: msto

README.md

@@ -47,5 +47,63 @@ fqgrep -r 'GACGAGATTA' -a 'GACGTGATTA' --r1-fastq /data/testR1.fastq.gz  --r2-fa
 See the following for usage:
 
 ```console
-fqgrep -h
+$ fqgrep -h
+fqgrep 1.0.3
+The fqgrep utility searches any given input FASTQ files, selecting records whose bases match one or more patterns.  By
+default, a pattern matches the bases in a FASTQ record if the regular expression (RE) in the pattern matches the bases.
+An empty expression matches every line.  Each FASTQ record that matches at least one of the patterns is written to the
+standard output.
+
+INPUT COMPRESSION
+
+By default, the input files are assumed to be uncompressed with the following exceptions: (1) If the input files are
+real files and end with `.gz` or `.bgz`, they are assumed to be GZIP compressed, or (2) if they end with `.fastq` or
+`.fq`, they are assumed to be uncompressed, or (3) if the `-Z/--decompress` option is specified then any unrecongized
+inputs (including standard input) are assumed to be GZIP compressed.
+
+THREADS
+
+The `--threads` option controls the number of threads used to _search_ the reads. Independently, for single end reads or
+interleaved paired end reads, a single thread will be used to read each input FASTQ.  For paired end reads across pairs
+of FASTQs, two threads will be used to read the FASTQs for each end of a pair.  Finally, a single thread will be created
+for the writer.
+
+EXIT STATUS
+
+The fqgrep utility exits with one of the following values: 0 if one or more lines were selected, 1 if no lines were
+selected, and >1 if an error occurred.
+
+USAGE:
+    fqgrep [FLAGS] [OPTIONS] [--] [args]...
+
+FLAGS:
+    -c, --count                 Only a count of selected lines is written to standard output
+    -F, --fixed-strings         Interpret pattern as a set of fixed strings
+    -v                          Selected lines are those not matching any of the specified patterns
+    -Z, --decompress            Assume all unrecognized inputs are GZIP compressed
+        --paired                Treat the input files as paired.  The number of input files must be a multiple of two,
+                                with the first file being R1, second R2, third R1, fourth R2, and so on.  If the pattern
+                                matches either R1 or R2, then both R1 and R2 will be output (interleaved).  If the input
+                                is standard input, then treat the input as interlaved paired end reads
+        --reverse-complement    Search the reverse complement for matches
+        --progress              Write progress information
+    -h, --help                  Prints help information
+    -V, --version               Prints version information
+
+OPTIONS:
+    -t, --threads <threads>     The number of threads to use for matching reads against pattern.  See the full usage for
+                                threads specific to reading and writing [default: 12]
+        --color <color>         Mark up the matching text.  The possible values of when are “never”, “always” and “auto”
+                                [default: never]
+    -e, --regexp <regexp>...    Specify a pattern used during the search of the input: an input line is selected if it
+                                matches any of the specified patterns.  This option is most useful when multiple `-e`
+                                options are used to specify multiple patterns
+    -f, --file <file>           Read one or more newline separated patterns from file.  Empty pattern lines match every
+                                input line.  Newlines are not considered part of a pattern.  If file is empty, nothing
+                                is matched
+
+ARGS:
+    <args>...    The first argument is the pattern to match, with the remaining arguments containing the files to
+                 match.  If `-e` is given, then all the arguments are files to match. Use standard input if either
+                 no files are given or `-` is given
 ```