Index a string in linux

https://unix.stackexchange.com/questions/303960/index-a-string-in-bash

Substring Extraction

${string:position}

Extracts substring from $string at $position.

If the $string parameter is "*" or "@", then this extracts the positional parameters, starting at $position.

${string:position:length}

Extracts $length characters of substring from $string at $position.

stringZ=abcABC123ABCabc
#       0123456789.....
#       0-based indexing.

echo ${stringZ:0}                       # abcABC123ABCabc
echo ${stringZ:1}                       # bcABC123ABCabc
echo ${stringZ:7}                       # 23ABCabc 

echo ${stringZ:7:3}                     # 23A
                                        # Three characters of substring.


# Is it possible to index from the right end of the string?

echo ${stringZ:-4}                      # abcABC123ABCabc
# Defaults to full string, as in ${parameter:-default}.
# However . . . 

echo ${stringZ:(-4)}                    # Cabc
echo ${stringZ: -4}                     # Cabc
# Now, it works.
# Parentheses or added space "escape" the position parameter.

Extract Reads From a Bam File That Fall Within A Given Region

https://www.biostars.org/p/48719/


# -h : include header
# file should be indexed.bam

samtools view -h input.indexed.bam "Chr1:10000-20000" > output.sam