Reads and parses a sam file.

    :param SAMfile: /path/to/file.sam
    :param header: logical, if True, reads the header information

    :returns: a pandas dataframe with the respective SAM columns: 'QNAME','FLAG','RNAME','POS','MAPQ','CIGAR','RNEXT','PNEXT','TLEN','SEQ','QUAL' and a list of the headers if header=True

def readSAM(SAMfile,header=False):
    """
    Reads and parses a sam file.

    :param SAMfile: /path/to/file.sam
    :param header: logical, if True, reads the header information

    :returns: a pandas dataframe with the respective SAM columns: 'QNAME','FLAG','RNAME','POS','MAPQ','CIGAR','RNEXT','PNEXT','TLEN','SEQ','QUAL' and a list of the headers if header=True

    """
    if header==True:
        f=open(SAMfile,"r+")
        head=[]
        for line in f.readlines():
            if line[0]=="@":
                head.append(line)
            else:
                continue
        f.close()

    sam=pd.read_table(SAMfile,sep="this_gives_one_column",comment="@",header=None)
    sam=pd.DataFrame(sam[0].str.split("\t").tolist())
    acols=[0,1,2,3,4,5,6,7,8,9]
    sam_=sam[acols]
    samcols=sam.columns.tolist()
    bcols=[ s for s in samcols if s not in acols ]
    sam_[10]=sam[bcols[0]]
    if len(bcols) > 1:
        for c in bcols[1:]:
            sam_[10]=sam_[10].astype(str)
            sam[c]=sam[c].astype(str)
            sam_[10]=sam_[10]+"\t"+sam[c]

    sam_.columns=['QNAME','FLAG','RNAME','POS','MAPQ','CIGAR','RNEXT','PNEXT','TLEN','SEQ','QUAL']

    if header==True:
        return sam_, head
    else:
        return sam_