int trim_sequenceQ(Fq_read *seq)
trims sequence based on lowQ base callings
Definition: trim.c:692
sequence manipulation for alignment
bool is_read_inBloom(Bfilter *tree_ptr, Fq_read *seq, Bfkmer *ptr_Bfkmer)
checks if a read is in Bloom filter. It computes the score for the read and returns true if it exceed...
Definition: trim.c:734
functions that implement the bloom filter
stores a fastq entry
Definition: fq_read.h:37
Construction of tree, check paths, write tree, read in tree.
int trim_adapter(Fq_read *seq, Ad_seq *adap_list)
trims sequence based on presence of N nucleotides
Definition: trim.c:628
Manipulation of Lmers and sequences.
bool is_read_inTree(Tree *tree_ptr, Fq_read *seq)
check if Lread is contained in tree. It computes the score for the read and its reverse complement; i...
Definition: trim.c:712
Bloom filter structure.
Definition: bloom.h:41
stores an adapter entry
Definition: adapters.h:38
fastq entries manipulations (read/write)
int trim_sequenceN(Fq_read *seq)
trims sequence based on presence of N nucleotides
Definition: trim.c:665
stores a processed kmer (2 bits pro nucleotide)
Definition: bloom.h:57
structure containing a T_ACGT-tree.
Definition: tree.h:60
int Qtrim_global(Fq_read *seq, int left, int right, char type)
trims left from the left and right from the right
Definition: trim.c:353