CMSC701-Project

Class project for CMSC701

Running this project

Generate index file using distance between access points as 524288 bytes

cd $PRJECT_ROOT
make main
./main.out build /path/to/compressed-fastq-file 524288

Get 10000 records starting from index 0

./main.out use /path/to/compressed-fastq-file /path/to/index-file 0 10000

Running our benchmark

cd $PRJECT_ROOT
make test_parser
./test_parser.out <fastq_file> <index_file> <num_consumer_threads> <num_producer_threads>

Commands to compile various benchmarks

1. FQFeeder

cd $PRJECT_ROOT
make fqfeeder
./fqfeeder.out /path/to/compressed-fastq-file <num_consumer_threads> <num_parsing_threads>

2. ../Scripts/CountBases.cpp

cd $PROJECT_ROOT
make baseline
./countbases.out /path/to/compressed-fastq-file

Installing zlib

git clone [email protected]:madler/zlib.git
cd zlib

./configure
make test

# if the above succeeds
make install

Generating test data

mkdir test-data
cd test-data

# 1.5 MB compressed
wget https://raw.githubusercontent.com/umd-cmsc701/project_0_test_data/main/test_input/salmonella.fa
gzip salmonella.fa

# 28 MB compressed
wget https://www.be-md.ncbi.nlm.nih.gov/Traces/sra-reads-be/fastq?acc=SRR28596297 -O ecoli.fq.gzip

# 595 MB compressed
wget https://www.be-md.ncbi.nlm.nih.gov/Traces/sra-reads-be/fastq?acc=SRR28592514 -O nematode.fq.gzip

About zran.c

(From https://github.com/madler/zlib/blob/master/examples/)

Illustrate the use of Z_BLOCK, inflatePrime(), and inflateSetDictionary() for random access of a compressed file. A file containing a raw deflate stream is provided on the command line. The compressed stream is decoded in its entirety, and an index built with access points about every SPAN bytes in the uncompressed output. The compressed file is left open, and can then be read randomly, having to decompress on the average SPAN/2 uncompressed bytes before getting to the desired block of data.

An access point can be created at the start of any deflate block, by saving the starting file offset and bit of that block, and the 32K bytes of uncompressed data that precede that block. Also the uncompressed offset of that block is saved to provide a reference for locating a desired starting point in the uncompressed stream. deflate_index_build() decompresses the input raw deflate stream a block at a time, and at the end of each block decides if enough uncompressed data has gone by to justify the creation of a new access point. If so, that point is saved in a data structure that grows as needed to accommodate the points.

To use the index, an offset in the uncompressed data is provided, for which the latest access point at or preceding that offset is located in the index. The input file is positioned to the specified location in the index, and if necessary the first few bits of the compressed data is read from the file. inflate is initialized with those bits and the 32K of uncompressed data, and decompression then proceeds until the desired offset in the file is reached. Then decompression continues to read the requested uncompressed data from the file.

There is some fair bit of overhead to starting inflation for the random access, mainly copying the 32K byte dictionary. If small pieces of the file are being accessed, it would make sense to implement a cache to hold some lookahead to avoid many calls to deflate_index_extract() for small lengths.

Another way to build an index would be to use inflateCopy(). That would not be constrained to have access points at block boundaries, but would require more memory per access point, and could not be saved to a file due to the use of pointers in the state. The approach here allows for storage of the index in a file.

Structs

• point represents an access point
  • Contains preceding 32K of uncompressed data for each access point
• deflate_index represents the index that is used to provide fast random access
  • Contains list of all access points

Original functions

• deflate_index_build: builds the index
  • Make one pass through a zlib, gzip, or raw deflate compressed stream and build an index, with access points about every span bytes of uncompressed output. gzip files with multiple members are fully indexed. span should be chosen to balance the speed of random access against the memory requirements of the list, which is about 32K bytes per access point. The return value is the number of access points on success (>= 1), Z_MEM_ERROR for out of memory, Z_BUF_ERROR for a premature end of input, Z_DATA_ERROR for a format or verification error in the input file, or Z_ERRNO for a file read error. On success, *built points to the resulting index.
• deflate_index_extract: uses the index to access len amount of data at some random offset
  • Use the index to read len bytes from offset into buf. Return the number of bytes read or a negative error code. If data is requested past the end of the uncompressed data, then deflate_index_extract() will return a value less than len, indicating how much was actually read into buf. If given a valid index, this function should not return an error unless the file was modified somehow since the index was generated, given that deflate_index_build() had validated all of the input. If nevertheless there is a failure, Z_BUF_ERROR is returned if the compressed data ends prematurely, Z_DATA_ERROR if the deflate compressed data is not valid, Z_MEM_ERROR if out of memory, Z_STREAM_ERROR if the index is not valid, or Z_ERRNO if there is an error reading or seeking on the input file.
• deflate_index_free: deallocates the index

Added functions

• deflate_index_save: saves index to file
• deflate_index_load: loads index from file

About kseq++

(From https://github.com/cartoonist/kseqpp)

kseq++ is a C++11 re-implementation of kseq.h. We have extended its functionality to also compute byte offsets from starting of compressed fastq file, for each record, which is stored in struct KSeq. Additionaly, we have extended its functionality to be able to parse fastq records from a native character stream. This allows it to be integrated when we read raw data from a random offset in compressed fastq file.