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C# - remove blocks of bytes in large binary files

i want a fast way in c# to remove a blocks of bytes in different places from binary file of size between 500MB to 1GB , the start and the length of bytes needed to be removed are in saved array
int[] rdiDataOffset= {511,15423,21047};
int[] rdiDataSize={102400,7168,512};
EDIT:
this is a piece of my code and it will not work correctly unless i put buffer size to 1:
while(true){
if (rdiDataOffset.Contains((int)fsr.Position))
{
int idxval = Array.IndexOf(rdiDataOffset, (int)fsr.Position, 0, rdiDataOffset.Length);
int oldRFSRPosition = (int)fsr.Position;
size = rdiDataSize[idxval];
fsr.Seek(size, SeekOrigin.Current);
}
int bufferSize = size == 0 ? 2048 : size;
if ((size>0) && (bufferSize > (size))) bufferSize = (size);
if (bufferSize > (fsr.Length - fsr.Position)) bufferSize = (int)(fsr.Length - fsr.Position);
byte[] buffer = new byte[bufferSize];
int nofbytes = fsr.Read(buffer, 0, buffer.Length);
fsr.Flush();
if (nofbytes < 1)
{
break;
}
}

No common file system provides an efficient way to remove chunks from the middle of an existing file (only truncate from the end). You'll have to copy all the data after the removal back to the appropriate new location.

A simple algorithm for doing this using a temp file (it could be done in-place as well but you have a riskier situation in case things go wrong).
Create a new file and call SetLength to set the stream size (if this is too slow you can Interop to SetFileValidData). This ensures that you have room for your temp file while you are doing the copy.
Sort your removal list in ascending order.
Read from the current location (starting at 0) to the first removal point. The source file should be opened without granting Write share permissions (you don't want someone mucking with it while you are editing it).
Write that content to the new file (you will likely need to do this in chunks).
Skip over the data not being copied
Repeat from #3 until done
You now have two files - the old one and the new one ... replace as necessary. If this is really critical data you might want to look a transactional approach (either one you implement or using something like NTFS transactions).
Consider a new design. If this is something you need to do frequently then it might make more sense to have an index in the file (or near the file) which contains a list of inactive blocks - then when necessary you can compress the file by actually removing blocks ... or maybe this IS that process.

If you're on the NTFS file system (most Windows deployments are) and you don't mind doing p/invoke methods, then there is a way, way faster way of deleting chunks from a file. You can make the file sparse. With sparse files, you can eliminate a large chunk of the file with a single call.
When you do this, the file is not rewritten. Instead, NTFS updates metadata about the extents of zeroed-out data. The beauty of sparse files is that consumers of your file don't have to be aware of the file's sparseness. That is, when you read from a FileStream over a sparse file, zeroed-out extents are transparently skipped.
NTFS uses such files for its own bookkeeping. The USN journal, for example, is a very large sparse memory-mapped file.
The way you make a file sparse and zero-out sections of that file is to use the DeviceIOControl windows API. It is arcane and requires p/invoke but if you go this route, you'll surely hide the uggles behind nice pretty function calls.
There are some issues to be aware of. For example, if the file is moved to a non-ntfs volume and then back, the sparseness of the file can disappear - so you should program defensively.
Also, a sparse file can appear to be larger than it really is - complicating tasks involving disk provisioning. A 5g sparse file that has been completely zeroed out still counts 5g towards a user's disk quota.
If a sparse file accumulates a lot of holes, you might want to occasionally rewrite the file in a maintenance window. I haven't seen any real performance troubles occur, but I can at least imagine that the metadata for a swiss-cheesy sparse file might accrue some performance degradation.
Here's a link to some doc if you're into the idea.

Set limit of text file

I am writing lines to text file. Is there a way to limit the maximum number of lines in a text file. So that I am not allowed to write after that limit.
Or
if i continue to write after the max line limit the oldest written lines are deleted to accommodate the newly added lines.

There is ... but you shouldn't be hitting it ... And if you ARE ... well, maybe a text file isn't what you're looking for.
Size wise, a file has different limitations depending on your file system ... NTFS (almost 16TB), FAT (fat 32 is almost 4GB), unix file systems will have their limitations, and so on ...
here you have answers about the size: one answer, and another
Like they suggest, your limit will be the size of the file.
As for your comment:
You can set the limit to whatever you wish.
What you do then is up to you ... if you decide to overwrite the file, it'll delete and start afresh. if you decide to append, it'll append to the end.
I would suggest create a queue of a 100 strings, and if you push new ones, drop the last one in the queue. Then you can just have that class save the log whenever, wherever and however you want.

Create your own method like this
public void writeLines(string filePath,string[] lines,int limit)
{
var buffer=Enumerable.Empty<string>();
if(File.Exists(filePath))
buffer=File.ReadAllLines(path);
File.WriteAllLines(filePath,lines);
int range=limit-lines.Length+buffer.Count;
File.AppendAllLines(filePath,buffer.Take(range));
}

The answer to the first question is very simple:
Know your storage limit.
Know your current file size.
If the new line's length plus current file size is more than the storage limit, don't append it.
Now, the second is kind of tricky. As pointed out by several participants on this thread, line-by-line threshold manipulation can be very very costly.
Let's do some napkin simulations, and assume you're inserting 1024 bytes (1KB) at each Append, and your storage limit is 1GB. Once you insert the last line (n. 1048576), you decide you need to remove the first line. There's a few ways to accomplish this, but the majority of them will involve loading the whole collection minus the initial line elsewhere (memory, disk, you name it) and Appending the new one. Not exactly the most practical approach - you'll be manipulating a stack a million times larger than the content you want to add, just for the sake of adding it.
Solution 1
Cursor buffer
On our example you have 1048576 possible entries (1KB records on 1GB file).
Start filling it up; save the current position (cursor) elsewhere.
Once you reach the limit, your cursor resets; you overwrite position 0, then 1, and so forth.
Advantages: Very low disk cost.
Disadvantages: You'll need to keep track of your current cursor somewhere.
Solution 2
Text blocks
Assume 1GB storage, and max 1MB files for this example.
Start filling up File #0.
Once it reaches 1MB, close it. Open File #1. Rinse and repeat.
Once you fill up file #1023 (thus reaching the 1GB max), delete oldest file (#0). Create file #1024. Continue your logging.
Advantages: Low manipulation cost - you only run one delete operation.
Disadvantages: You don't delete only one entry - you delete a whole block.

Reading a MemoryStream which contains multiple files

If I have a single MemoryStream of which I know I sent multiple files (example 5 files) to this MemoryStream. Is it possible to read from this MemoryStream and be able to break apart file by file?
My gut is telling me no since when we Read, we are reading byte by byte... Any help and a possible snippet would be great. I haven't been able to find anything on google or here :(

You can't directly, not if you don't delimit the files in some way or know the exact size of each file as it was put into the buffer.
You can use a compressed file such as a zip file to transfer multiple files instead.

A stream is just a line of bytes. If you put the files next to each other in the stream, you need to know how to separate them. That means you must know the length of the files, or you should have used some separator. Some (most) file types have a kind of header, but looking for this in an entire stream may not be waterproof either, since the header of a file could just as well be data in another file.
So, if you need to write files to such a stream, it is wise to add some extra information. For instance, start with a version number, then, write the size of the first file, write the file itself and then write the size of the next file, etc....
By starting with a version number, you can make alterations to this format. In the future you may decide you need to store the file name as well. In that case, you can increase version number, make up a new format, and still be able to read streams that you created earlier.
This is of course especially useful if you store these streams too.

Since you're sending them, you'll have to send them into the stream in such a way that you'll know how to pull them out. The most common way of doing this is to use a length specification. For example, to write the files to the stream:
write an integer to the stream to indicate the number of files
Then for each file,
write an integer (or a long if the files are large) to indicate the number of bytes in the file
write the file
To read the files back,
read an integer (n) to determine the number of files in the stream
Then, iterating n times,
read an integer (or long if that's what you chose) to determine the number of bytes in the file
read the file

You could use an IEnumerable<Stream> instead.

You need to implement this yourself, what you would want to do is write in some sort of 'delimited' into the stream. As you're reading, look for that delimited, and you'll know when you have hit a new file.
Here's a quick and dirty example:
byte[] delimiter = System.Encoding.Default.GetBytes("++MyDelimited++");
ms.Write(myFirstFile);
ms.Write(delimiter);
ms.Write(mySecondFile);
....
int len;
do {
len = ms.ReadByte(buffer, lastOffest, delimiter.Length);
if(buffer == delimiter)
{
// Close and open a new file stream
}
// Write buffer to output stream
} while(len > 0);

transpose csv file with C# or other program

I'm using C# and I write my data into csv files (for further use). However my files have grown into a large scale and i have to transpose them. what's the easiest way to do that. in any program?
Gil

In increasing order of complexity (and also increasing order of ability to handle large files):
Read the whole thing into a 2-D array (or jagged array aka array-of-arrays).
Memory required: equal to size of file
Track the file offset within each row. Start by finding each (non-quoted) newline, storing the current position into a List<Int64>. Then iterate across all rows, for each row: seek to the saved position, copy one cell to the output, save the new position. Repeat until you run out of columns (all rows reach a newline).
Memory required: eight bytes per row
Frequent file seeks scattered across a file much larger than the disk cache results in disk thrashing and miserable performance, but it won't crash.
Like above, but working on blocks of e.g. 8k rows. This will create a set of files each with 8k columns. The input block and output all fit within disk cache, so no thrashing occurs. After building the stripe files, iterate across the stripes, reading one row from each and appending to the output. Repeat for all rows. This results in sequential scan on each file, which also has very reasonable cache behavior.
Memory required: 64k for first pass, (column count/8k) file descriptors for second pass.
Good performance for tables of up to several million in each dimension. For even larger data sets, combine just a few (e.g. 1k) of the stripe files together, making a smaller set of larger stripes, repeat until you have only a single stripe with all data in one file.
Final comment: You might squeeze out more performance by using C++ (or any language with proper pointer support), memory-mapped files, and pointers instead of file offsets.

It really depends. Are you getting these out of a database? The you could use a MySql import statement. http://dev.mysql.com/doc/refman/5.1/en/load-data.html
Or you could use could loop through the data add it to a file stream using streamwriter object.
StreamWriter sw = new StreamWriter('pathtofile');
foreach(String[] value in lstValueList){
String something = value[1] + "," + value[2];
sw.WriteLine(something);
}

I wrote a little proof-of-concept script here in python. I admit it's buggy and there are likely some performance improvements to be made, but it will do it. I ran it against a 40x40 file and got the desired result. I started to run it against something more like your example data set and it took too long for me to wait.
path = mkdtemp()
try :
with open('/home/user/big-csv', 'rb') as instream:
reader = csv.reader(instream)
for i, row in enumerate(reader):
for j, field in enumerate(row):
with open(join(path, 'new row {0:0>2}'.format(j)), 'ab') as new_row_stream:
contents = [ '{0},'.format(field) ]
new_row_stream.writelines(contents)
print 'read row {0:0>2}'.format(i)
with open('/home/user/transpose-csv', 'wb') as outstream:
files = glob(join(path, '*'))
files.sort()
for filename in files:
with open(filename, 'rb') as row_file:
contents = row_file.readlines()
outstream.writelines(contents + [ '\n' ])
finally:
print "done"
rmtree(path)

C# code to perform Binary search in a very big text file

Is there a library that I can use to perform binary search in a very big text file (can be 10GB).
The file is a sort of a log file - every row starts with a date and time. Therefore rows are ordered.

I started to write the pseudo-code on how to do it, but I gave up since it may seem condescending. You probably know how to write a binary search, it's really not complicated.
You won't find it in a library, for two reasons:
It's not really "binary search" - the line sizes are different, so you need to adapt the algorithm (e.g. look for the middle of the file, then look for the next "newline" and consider that to be the "middle").
Your datetime log format is most likely non-standard (ok, it may look "standard", but think a bit.... you probably use '[]' or something to separate the date from the log message, something like [10/02/2001 10:35:02] My message ).
On summary - I think your need is too specific and too simple to implement in custom code for someone to bother writing a library :)

As the line lengths are not guaranteed to be the same length, you're going to need some form of recognisable line delimiter e.g. carriage return or line feed.
The binary search pattern can then be pretty much your traditional algorithm. Seek to the 'middle' of the file (by length), seek backwards (byte by byte) to the start of the line you happen to land in, as identified by the line delimiter sequence, read that record and make your comparison. Depending on the comparison, seek halfway up or down (in bytes) and repeat.
When you identify the start index of a record, check whether it was the same as the last seek. You may find that, as you dial in on your target record, moving halfway won't get you to a different record. e.g. you have adjacent records of 100 bytes and 50 bytes respectively, so jumping in at 75 bytes always takes you back to the start of the first record. If that happens, read on to the next record before making your comparison.
You should find that you will reach your target pretty quickly.

You would need to be able to stream the file, but you would also need random access. I'm not sure how you accomplish this short of a guarantee that each line of the file contains the same number of bytes. If you had that, you could get a Stream of the object and use the Seek method to move around in the file, and from there you could conduct your binary search by reading in the number of bytes that constitute a line. But again, this is only valid if the lines are the same number of bytes. Otherwise, you would jump in and out of the middle of lines.
Something like
byte[] buffer = new byte[lineLength];
stream.Seek(lineLength * searchPosition, SeekOrigin.Begin);
stream.Read(buffer, 0, lineLength);
string line = Encoding.Default.GetString(buffer);

This shouldn't be too bad under the constraint that you hold an Int64 in memory for every line-feed in the file. That really depends upon how long the line of text is on average, given 1000 bytes per line you be looking at around (10,000,000,000 / 1000 * 4) = 40mb. Very big, but possible.
So try this:
Scan the file and store the ordinal offset of each line-feed in a List
Binary search the List with a custom comparer that scans to the file offset and reads the data.

If your file is static (or changes rarely) and you have to run "enough" queries against it, I believe the best approach will be creating "index" file:
Scan the initial file and take the datetime parts of the file plus their positions in the original (this is why has to be pretty static) encode them some how (for example: unix time (full 10 digits) + nanoseconds (zero-filled 4 digits) and line position (zero filed 10 digits). this way you will have file with consistent "lines"
preform binary search on that file (you may need to be a bit creative in order to achieve range search) and get the relevant location(s) in the original file
read directly from the original file starting from the given location / read the given range
You've got range search with O(log(n)) run-time :) (and you've created primitive DB functionality)
Needless to say that if the file data file is updated "too" frequently or you don't run "enough" queries against the index file you mat end up with spending more time on creating the index file than you are saving from the query file.
Btw, working with this index file doesn't require the data file to be sorted. As log files tend to be append only, and sorted, you may speed up the whole thing by simply creating index file that only holds the locations of the EOL marks (zero-filled 10 digits) in the data file - this way you can preform the binary search directly on the data-file (using the index file in order to determinate the seek positions in the original file) and if lines are appended to the log file you can simply add (append) their EOL positions to the index file.

The List object has a Binary Search method.
http://msdn.microsoft.com/en-us/library/w4e7fxsh%28VS.80%29.aspx