Calculate the number of bases in the read trimmed by BWA

calculate if this read is low quality

* calc_vdb() - returns value between zero (most biased) and one (no bias) * on success, or HUGE_VAL when VDB cannot be calculated beca

calculate average mappability for a transcript's TSS region: [TSS-width, TSS+width], body region: [start+width+1, end-width-1], TE

in principle, this function is only for ChIP-seq target experiment should make target and control inherit from ChIPSeqExperiment, will do

Returns: 0 on success (BGZF header); -1 on non-BGZF GZIP header; -2 on error

trim heading and tailing ambiguous bases; mark deleted and remove sequence

Removes duplicate records from the buffer. The meaning of "duplicate" is controlled by the $collapse variable, which can cause that from multiple

These stats should only be calculated for the original reads ignoring supplementary artificial reads otherwise we'll accidentally double count

construct Transcript from the 6 lines from RSEM .TI file

* Converts a cram_block_compression_hdr struct used for decoding to * one used for encoding. Maybe this should be a transparent * operation applied

* CRAM files don't store the RG:Z:ID per read in the aux field. * Instead they have a numerical data series (RG) to point each read * back to the Nt

* Check the files are consistent and capable of being concatenated. * Also fills out the rg2id read-group hash and the version numbers * and produce

* Closes a CRAM file. * Returns 0 on success * -1 on failure */

* cram_codec structures are specialised for decoding or encoding. * Unfortunately this makes turning a decoder into an encoder (such as * when trans

* Applies various compression methods to specific blocks, depending on * known observations of how data series compress. * * Returns 0 on success

Returns true if the container is empty (EOF marker) */

Sets the landmarks[] array (pointer copy, not a memory dup) and * num_landmarks value. */

* Decodes the Tag Dictionary record in the preservation map * Updates the cram compression header. * * Returns number of bytes decoded on success

* Attempts to estimate the size of some blocks so we can preallocate them * before decoding. Although decoding will automatically grow the blocks,

* Internal part of cram_decode_slice(). * Generates the sequence, quality and cigar components. */

* Spawn a multi-threaded version of cram_decode_slice(). */

Resolve mate pair cross-references between recs within this slice */

* Note we also need to scan through the record encoding map to * see which data series share the same block, either external or * CORE. For example

* Encodes auxiliary data. Largely duplicated from above, but done so to * keep it simple and avoid a myriad of version ifs. * * Returns the read-gr

* Encodes auxiliary data. * Returns the read-group parsed out of the BAM aux fields on success * NULL on failure or no rg present (FIXME) *

* Encodes a single slice from a container * * Returns 0 on success * -1 on failure */

* Encodes a slice compression header. * * Returns cram_block on success * NULL on failure */

* Encodes a single read. * * Returns 0 on success * -1 on failure */

* Read the next cram record and return it. * Note that to decode cram_record the caller will need to look up some data * in the current slice, point

* Builds an index file. * * fd is a newly opened cram file that we wish to index. * fn_base is the filename of the associated CRAM file. * fn_idx