Multiple Files

Multiple files

• gsufsort supports multiple files in directory INPUT (command --dir):

For example, dataset/input.txt were splitted into 5 files in dataset/input/:

ls dataset/input/
input-1.txt  input-2.txt  input-3.txt  input-4.txt  input-5.txt

One can index all files in dataset/input/ with options --dir and --sa:

./gsufsort dataset/input/ --dir --sa

In the case no argument is given for --output, the default output filename is ./all.

## gsufsort ##
## store_to_disk ##
all.4.sa 	20198960 bytes (n = 5049740)

Compare the output all.4.sa with dataset/input.txt.4.sa:

diff all.4.sa dataset/input.txt.4.sa -s
Files all.4.sa and dataset/input.txt.4.sa are identical

We can also output the concatenations of all files in all.str (option --str):

./gsufsort dataset/input/ --dir --sa

## gsufsort ##
## store_to_disk ##
all.1.str 5049740  bytes (n = 5049740)

When we compare all.str with dataset/input.txt, there is an extra byte in all.str corresponding to the terminator # added to the concatenated string:

ls all.1.str dataset/input.txt -la
-rw-rw-r--. 1 louza louza 5049740 Jun 26 09:54 all.1.str
-rw-rw-r--. 1 louza louza 5049739 Jun 25 10:19 dataset/input.txt

diff all.1.str dataset/input.txt -s
10001d10000
<

• Awarning: in the case one use options --txt, --fasta or -fastq together with --dir, be carefull that INPUT contains only valid files, otherwise the program may crash.