File alignment

This is the most basic, human readable format of the three. This is generated by almost every alignment algorithm that exists. It consists of a header, a row for every read in your dataset, and 11 tab-delimited fields describing that read. The header varies in size but adheres to a particular format depending on what information you decide to add.

Some example information that can be entered into the header is: command that generated the SAM file, SAM format version, sequencer name and version. The full list of available header fields can be found below. The bitwise flag is a lookup code to explain certain features about the particular read exact same concept as Linux permission codes! The big advantage is that you don't pay for data or code that you don't use.

Also the reason that reading [attributes] is expensive when you read it the first time. The relevance of the file alignment is how the raw data in the sections line up. Most modern executables that contain machine code use an alignment of bytes, the size of a virtual memory page. That isn't very relevant for assemblies containing managed code, IL is just data.

Which would make it sense to use a smaller alignment, one that wastes less space. The only possible reason I can think of for adding the option to the UI at all is that the C compiler has very few compile options compared to other compilers.

So the option is there because the compiler has the option. A lot of the tweaks are covered by [attributes], nicely making the compiler command line short and snappy. But no attribute for the file alignment, it needs to be known before generating the file, an attribute would be too late.

But still not covering them all, the really obscure ones have to be set in the "Command Line" option page. Stack Overflow for Teams — Collaborate and share knowledge with a private group.

Create a free Team What is Teams? Collectives on Stack Overflow. Learn more. For what reason would I choose a C compiler file alignment setting other than ? Ask Question. If set to none , the error will be reported only in the compiler's text output. Specifies whether an integer arithmetic statement that is not in the scope of the checked or unchecked keywords and that results in a value outside the range of the data type will cause a run-time exception. Specifies whether mscorlib.

Check this box if you want to define or create your own System namespace and objects. Specifies the type of debugging information generated by the compiler.

For information on how to configure the debug performance of an application, see Making an Image Easier to Debug. This setting has the following options:. Allows source code debugging when the program is started in the debugger but will only display assembler when the running program is attached to the debugger.

Produces a. PDB file, a non-platform-specific, portable symbol file that provides other tools, especially debuggers, information about what is in the main executable file and how it was produced. Select the Edit Select All menu command to select all site s for every sequence in the data set. Select Alignment Align by ClustalW from the main menu to align the selected sequences data using the ClustalW algorithm.

Once the alignment is complete, s ave the current alignment session by selecting Data Save Session from the main menu. This will allow the current alignment session to be restored for future editing. Align ing Sequences U sing Muscle. Here we describe how to create a multiple sequence alignment using the Muscle option.

Select Create a new alignment and then select DNA. On the Alignment Explorer launch bar , you will find an icon that looks like a flexing arm.