HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools.
A set of sample programs are available which showcases the usage of APIs in HTSlib. They are based on version 1.17 of HTSLib and are mainly for demonstration of API usage. Further optimization and error handling might be required for actual usage.
GCC and compatible compilers can be used to build these samples.
A makefile is available along with source files which links statically to htslib. To use dynamic linking, update the makefile's 'LDFLAGS' and 'rpath' path. The 'rpath' path to be set as the path to lib directory of htslib installation.
# linking statically on a linux machine
gcc -g -o <binary name> <source name> -I <htslib include path> \
<htslib lib path>/libhts.a -lcrypto -lm -lpthread -lcurl -llzma -lz -lbz2
# dynamically linking with libhts
gcc -g -o <binary name> <source name> -I <htslib include path> \
-L <htslib lib path> -lhts -Wl,-rpath,<htslib lib path>
In many cases, the alignment data are expected as sorted, compressed and indexed.
This application showcases the basic read of alignment files and flag access. It reads and shows the count of read1 and read2 alignments.
This application showcases the basic read and write of alignment data. It saves the read1 and read2 as separate files in given directory, one as sam and other as bam.
This application showcases the output file format selection. It saves the read1 and read2 as separate files in given directory, both as compressed sam though the extensions are different.
This application showcases the different way in which cram reference data is used for cram output creation.
This application showcases the fasta/fastq data read.
This application showcases the read and access of header data. It can show all header line of given type, data of a given tag on a specific header line or for all lines of given type.
This application showcases the read and access of header data. It shows all reference names which has length equal or greather to given input.
This application showcases read of different alignment data fields. It shows contents of each alignment.
This application showcases read of specific auxiliary tag data in alignment. It shows the data retrieved using 2 APIs, one as a string with tag data and other as raw data alternatively.
This application showcases read of all auxiliary tag data one by one in an alignment. It shows the data retrieved.
This application showcases the write of header lines to a file. It adds header line of types, SQ, RG, PG and CO and writes to standard output.
This application showcases removal of header line from a file. It removes either all header lines of given type or one specific line of given type with given unique identifier. Modified header is written on standard output.
This application shows the update of header line fields, where update is allowed. It takes the header line type, unique identifier for the line, tag to be modified and the new value. Updated data is written on standard output.
This application showcases the update of alignment data. It takes alignment name, position of field to be modified and new value of it. Modified data is written on standard output.
This application showcases the update of auxiliary data in alignment. It takes alignment name, tag to be modified, its type and new value. Modified data is written on standard output.
This application showcases the update of auxiliary array data in alignment. It adds count of ATCGN base as an array in auxiliary data, BA:I. Modified data is written on standard output.
This application showcases the fasta/fastq data write. It appends a dummy data to given file.
This application showcases the creation of index along with output creation. Based on file type and shift, it creates bai, csi or crai files.
This application showcases the usage of region specification in alignment read.
This application showcases the usage of mulitple region specification in alignment read.
This application showcases the pileup api, where all alignments covering a reference position are accessed together. It displays the bases covering each position on standard output.
This application showcases the mpileup api, which supports multiple input files for pileup and gives a side by side view of them in pileup format. It displays the bases covering each position on standard output.
This application showcases the access of base modifications in alignment. It shows the modifications present in an alignment and accesses them using available APIs. There are 2 APIs and which one to be used can be selected through input.
This application showcases the base modification access in pileup mode. It shows the pileup display with base modifications.
This application showcases the read of selected fields alone, reducing the overhead / increasing the performance. It reads the flag field alone and shows the count of read1 and read2. This has impact only on CRAM files.
This application showcases the use of threads in file handling. It saves the read1 and read2 as separate files in given directory, one as sam and other as bam. 2 threads are used for read and 1 each dedicated for each output file.
This application showcases the use of thread pool in file handling. It saves the read1 and read2 as separate files in given directory, one as sam and other as bam. A pool of 4 threads is created and shared for both read and write.
More detailed documentation is available in the DEMO.md with worked examples per demonstration tool.