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samtools view -h -b sample_sorted.bam "chr1:10-13" > tiny_sorted.bam. Extract the same reads as above, but instead of displaying them, writes them to a new bam file, tiny_sorted.bam. The -b option makes the output compressed and the -h option causes the SAM headers to be output also.
Changes made to the command line environment after SetLocal commands are local to the batch file. EndLocal command restores the previous settings. [17] The Call command allows subroutines within batch file. The Call command in COMMAND.COM only supports calling external batch files. File name parser extensions to the Set command are comparable ...
Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [1] it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. [ 2 ] [ 3 ] BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments ...
COMMAND.COM is the default command-line interpreter for MS-DOS, Windows 95, Windows 98 and Windows Me.In the case of DOS, it is the default user interface as well. [2] It has an additional role as the usual first program run after boot (init process), hence being responsible for setting up the system by running the AUTOEXEC.BAT configuration file, and being the ancestor of all processes.
Starting with Windows 95, the Run command is accessible through the Start menu and also through the shortcut key ⊞ Win+R.Although the Run command is still present in Windows Vista and later, it no longer appears directly on the Start menu by default, in favor of the new search box and a shortcut to the Run command in the Windows System sub-menu.
Non-English file names work only if entered through a DOS character set compatible editor. File names with characters outside this set do not work in batch files. To get a command prompt with Unicode instead of Code page 437 or similar, one can use the cmd /U command. In such a command prompt, a batch file with Unicode filenames will work.
Command-line completion allows the user to type the first few characters of a command, program, or filename, and press a completion key (normally Tab ↹) to fill in the rest of the item. The user then presses Return or ↵ Enter to run the command or open the file.
The command-syntax on Microsoft Windows and ReactOS is: type [Drive:][Path]FileName [Drive:][Path]FileName – This parameter specifies the location and name of the file or files to view. Multiple file names need to be separated with spaces. /? – This parameter displays help for the command.