modify format

README.md

@@ -27,43 +27,61 @@ Align read to its primitive location in Reference
 deBGA index   
 -k,                     INT the k-mer length of the vertices of RdBG. This is a basic parameter for building theRdBG-index. For the current version of deBGA, 
 							the range of -k parameter is restricted to 21-28 bp, considering both of the effectiveness of the seeds and memory footprint[22]. 
-    
+ 
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 deBGA aln 
 -k,                     INT the minimum length of a valid Uni-MEM seed. For current version of deBGA, this setting should be equal to the k-mer length of the RdBG-index[22].    
+
 -s,                     INT the number of iterations of re-seeding. deBGA iteratively aligns a read in at most (-s + 1) iterations with various set of seeds. 
 							This parameter works combining with the minimum interval of seeding (the -i option) and the maximum allowed number of hits per seed (the -n option). 
 							That is, in the r-th iteration (r = 1 ,…, -s), deBGA tries to generate seeds at every ((-s)– r +1)*(-i) bp along the read. 
 							If the read still cannot be successfully aligned after -s iterations, deBGA would ignore -n option to handle very repetitive reads in the (-s+1)-th iteration[4].    
+
 -i,                     INT the minimum interval of seeding. This parameter determines the density of seeds, which is related to the sensitivity and efficiency of alignment. 
 							Configuring this parameter with lower value will make deBGA generate seed more densely, which could improve the sensitivity, but at the expense of throughput[5].   
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 -n,                     INT the maximum allowed number of hits per seed. In the first -s iterations of the alignment process, the seeds with more than -n hits would be discarded for achieving faster speed.
-							DeBGA ignores this restriction to introduce repetitive seeds if the read still cannot be successfully aligned after -s iterations[300].    
+							DeBGA ignores this restriction to introduce repetitive seeds if the read still cannot be successfully aligned after -s iterations[300].  
+							
 -c,                     NUM the threshold on the edit distance for early stop. In each iteration, deBGA checks the edit distance of the obtained best alignment. 
 							If the ratio ED_best/RL <(-c), where ED_best and RL are respectively the edit distance of the best alignment and the read length, 
 							deBGA considers that the read is confidently aligned and early-stops the alignment[0.05].    
+
 --cl,                   NUM the adjusted threshold on the edit distance for early stop. When --cl option is set, in any given iteration, if there is at least one Uni-MEM seed available for extension, 
 							but no successful alignment is obtained, the threshold on the edit distance(-c) can be dynamically adjusted to the value of --cl in next iterations. 
 							This is a heuristic may acceleratethe alignment ofdivergent reads, e.g., reads having many low quality bases. 
 							If --cl is not set, there will be no change on the -c option during the process (default: following the setting of -c).    
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 --local,                    the local alignment option for confident alignment. When --local option is set, in any given iteration, if there is at least one Uni-MEM seed available for extension, 
 							but no successful alignment is obtained,deBGA perform local alignment instead of end-to-end alignment in following iterations.The best obtained local alignment will be output as the result. 
 							It is also worthnoting that the --cl option and --local option should not be simultaneously set (default: not set).    
+
 --local-match,          INT the score for a matched base in the local alignment.This option will take effect only if --local option is set[1].     
+
 --local-mismatch,       INT the penalty for a mismatched base in the local alignment. This option will take effect only if --local option is set[4].    
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 --local-gap-open,       INT the penalty for a gap open in the local alignment.This option will take effect only if --local option is set[6].    
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 --local-gap-extension,  INT the penalty for gap extension in the local alignment.This option will take effect only if --local option is set[1].     
+
 -u,                     INT the upper limit of insert size. For a pair-end read, deBGA pairs the alignments of the two ends according to the upper (-u option) and lower (-f option) limits of the insert size.
 							deBGA will consider it as a suitable pair-end alignment only if the inferred insert size is within the range [-f, -u][1000].
+
 -f,                     INT the lower limit of insert size. For a pair-end read, deBGA pairs the alignments of the two ends according to the upper (-u option) and lower (-f option) limits of the insert size. 
 							deBGA will consider it as a suitable pair-end alignment only if the inferred insert size is within the range [-f, -u][50].        
+
 -o,                     INT the maximum number of alignment output.deBGA outputs at most -o alignments for the read. This is except for the pair-end reads which are handled with the anchoring alignment strategy. 
 							For thosereads, the number of outputsis determined by the -x option[20].  
+
 -x,                     INT the maximum number of alignment output for anchoring alignment. For the pair-end reads aligned with the anchoring alignment strategy, deBGA will output at most -x alignments[150].    
+
 -l,                     INT the maximum allowed read length. For the current version of deBGA, reads shorter than -l bp will be normally processed, andfor reads longer than -l bp, only the first -l bp will be aligned, 
 							and the other parts will be trimmed. Set -l option with a larger number may slightly increasethememory footprint. For most nowadays next generation sequencing reads, e.g., reads from Illumina platforms, 
 							the default setting is long enough to work withoutthe trimming. Moreover, the current version ofdeBGA can support reads upto 4096 bp (setting -l to 4096)[512].     
+
 -e,                     INT the budget for single-end alignment. In single-end read alignment, deBGA sets a budget on the computation resource in advance for balancing the efficiency and the sensitivity. More precisely, in the extension phase, 
 							deBGA subsequently extend the candidate seeds in order of their coverage lengths, until more than -e extension operations have been totally executed after handling some of the seeds, or all the seeds are extended[100].
+
 -p,                     INT the number of threads. The current version of deBGA supports upto 32 threads in read alignment[1].    
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