|  |  | 
    |  |  | 
    | TPRead | 
        
          | getTPRead(alngt,
        compareList,
        readdic) Funtion which transforms an HTSeq alignment to a TPRead class.
 | source code |  | 
    | CustomRead | 
        
          | getCustomRead(alngt,
        compareList,
        readdic) Funtion which transforms an HTSeq alignment to a CustomRead class.
 | source code |  | 
    | dictionary | 
        
          | GetOrderDictionary(referenceSAM) Function to get a dictionary containing the rank of a read (given a 
      sorted samfile by readname, samtools).
 | source code |  | 
    | Readobj |  | 
    | gaps,mismatches |  | 
    | (bool,list,bool) | 
        
          | getAllID(textfile,
        read,
        compareList,
        readdic) Reads all alignments for the current read which are in the SAM file 
      (sorted).
 | source code |  | 
    | np.array | 
        
          | CompareAlignments(reflist,
        artlist,
        file) Compares alignments for the reference and artificial reference for a 
      specific read id.
 | source code |  | 
    | read obj. | 
        
          | SkipHeader(file,
        compareList,
        readdic) Skips the header from a SAM file, but reads the first line of the 
      alignment section.
 | source code |  | 
    | int,int | 
        
          | getRanks(RefRead,
        ArtRead,
        rankdic) Function which returns the ranks of 2 given readIDs (read from 
      reference,read from artificial).
 | source code |  | 
    | ranks |  | 
    | int |  | 
    | int |  | 
    | float |  | 
    | float |  | 
    | int |  | 
    | readobj, readname | 
        
          | isSaneAlignment(alignment,
        identifier,
        compareList,
        readdic) Checks alignment line for unnecessary informations to skip
 | source code |  | 
    | bool |  | 
    | int | 
        
          | getHammingdistance(CompareString,
        start,
        end) Computes the number of subsitutions in the artificial reference using
      the CompareString.
 | source code |  | 
    | dictionary | 
        
          | readReadQualities(fastqfile) Reads a .fastqfile and calculates a defined readscore input: fastq 
      file output: fastq dictionary key = readid; value = qualstr
 | source code |  | 
    | dictionary | 
        
          | extendReadDic(readdic) Extends a given dictionary with KEY = readid and VALUE = qualstr such
      that an internal naming is generated which can be used to efficiently
      create an numpy array
 | source code |  | 
    | string |  | 
    | list | 
        
          | CreateCompareList(Reference,
        ARG) Creates a list which is used for comparisons between aligned reads 
      (exact number of mismatches)
 | source code |  | 
    | read obj. | 
        
          | readSAMline(alignment,
        identifier,
        compareList,
        readdic) Function for reading SAM alignment text file (one line)
 | source code |  | 
    | int |  | 
    | array |  | 
    |  |  | 
    |  | 
        
          | writeToTabRef(RefArray,
        outfile,
        reverseReadArray,
        ReadDic) Write function for hits ont he reference genome.
 | source code |  | 
    | np.array(obj) |  | 
    | files |  | 
    |  |  | 
    |  | 
        
          | initOutFiles(controlDic,
        mapper,
        outpath) Since we append in the program, we need to make sure no old files 
      remain...
 | source code |  |