FastqPuri
src Directory Reference
Directory dependency graph for src:
src

Files

file  adapters.c
 sequence manipulation for alignment
 
file  bloom.c
 functions that implement the bloom filter
 
file  city.c
 functions for hashin strings, C translation of cityhash (C++, google)
 
file  fa_read.c
 reads in and stores fasta files
 
file  fopen_gen.c
 Uncompress/compress input/output files using pipes.
 
file  fq_read.c
 fastq entries manipulations (read/write)
 
file  init_makeBloom.c
 Help dialog for makeBloom and initialization of the command line arguments.
 
file  init_makeTree.c
 Help dialog for makeTree and initialization of the command line arguments.
 
file  init_Qreport.c
 Help dialog for Qreport and initialization of the command line arguments.
 
file  init_Sreport.c
 Help dialog for Sreport and initialization of the command line arguments.
 
file  init_trimFilter.c
 help dialog for trimFilter and initialization of the command line arguments.
 
file  init_trimFilterDS.c
 help dialog for trimFilterDS and initialization of the command line arguments.
 
file  io_trimFilter.c
 buffer fq output, write summary file
 
file  Lmer.c
 Manipulation of Lmers and sequences.
 
file  makeBloom.c
 makeBloom main function
 
file  makeTree.c
 makeTree main function
 
file  Qreport.c
 QReport main function.
 
file  Rcommand_Qreport.c
 get Rscript command for Qreport
 
file  Rcommand_Sreport.c
 get Rscript command for Sreport
 
file  Sreport.c
 Sreport main function.
 
file  stats_info.c
 Construct the quality report variables and update them.
 
file  str_manip.c
 functions that do string manipulation
 
file  struct_trimFilter.c
 function that frees the memory of parTF (structure storing the trimFilter/trimFilterDS input arguments).
 
file  tree.c
 Construction of tree, check paths, write tree, read in tree.
 
file  trim.c
 trims/filter sequences after Quality, N's contaminations.
 
file  trimDS.c
 trim adapters from double stranded data
 
file  trimFilter.c
 trimFilter main function
 
file  trimFilterDS.c
 trimFilterDS main function