Changed folder structure

Makefile

@@ -18,8 +18,8 @@ LIBOBJ = \
 	lib/file.o\
 	lib/suffix_array.o\
 	external/malloc_count/malloc_count.o\
-	src/gsais.o\
-	src/gsaca-k.o
+	gsais.o\
+	gsaca-k.o
 
 all: compile
 

README.md

@@ -4,17 +4,32 @@ This code is an implementation of gSAIS and gSACA-K, which are modifications of
 SAIS [1] and SACA-K [2] algorithms to compute the generalized suffix array,
 maintaining their theoretical bounds and improving their practical performance
 
-#run:
+--
+**Settings:**
+
+We have implemented six MODEs in main.c:
+
+* 1: SAIS\* 
+* 2: SACA-K\* 
+* 3: SAIS  
+* 4: SACA-K 
+* 5: gSAIS
+* 6: gSACA-K
+
+\* uses integer alphabet as input.
+
+--
+##run:
 
 To run a test type:
 
 ```sh
 make
-make run DIR=dataset INPUT=input.1000.txt K=1000 MODE=1
+make run DIR=dataset INPUT=uniprot.100.fasta K=100 MODE=6
 ```
 
 
-#Experimental results
+##Experimental results
 
 
 **Collections:**

dataset/input.1000.txt

@@ -1,5 +1,3 @@
-BANANA
-CG
 GTTTCTGGACCACGTTCTCGCGAACGTTACCGAAATCACGCTGAAGGTCAGGGGCCGGCAAGAACATCGTTAGCGGTGTATG
 CTTTTAACC
 ATCGATTCTGGC

dataset/reads.10.fastq

@@ -0,0 +1,41 @@
+@SRR067577.3006/1
+CAATCTATTTAAAGTAATCCCTTGCACCTCTTATGCTCCCCCACAGCCCTTATAATATTTTAAGAGCATGTCTTTTTGTTTACATTTTTCCCATTAAAT
++
+IIIHIHIIIIIIIIHIHIHIIHIIIHGGIIIIIGHHIIIIHIHHIFIBIEDHFFFGGGEHD0BB>E@BCEDEGDECACF9CCBBEB>B@>??<A;??;A
+@SRR067577.3000/1
+AAGAAATGAGAAGTAATCAGAAAACCACTTAAGGTGAATGGAAATAGGGACACAGCATACCAAAACTTAGGGATGCAGTAGAAGCAGTGCTTAGC
++
+IGIIIIIIIIIHHIIIIIHIIGIIIIIIIBGGGGBIHEIIHGGGHHGDEGEGHGGGEEGHBBBBBD@@CBA>B@E><3/<??;??;<6=>0<<;@
+@SRR067577.3040/1
+GATATATTTTTCCTTAGTTTAAAAATTAGATGGATTTTGAGGTTCTCCTTCTACTTTTTAAGTATATTCTGAAGTATTACAAATCATTGATATATGCCA
++
+IIIIIIIIIIIIIHIIIHIIGIIIIDIIIEHIIIIIFIHBIIGIIDIIEHIGIFIIIIIIIIHHIIIIHGIBFBGFIHIGDGHDG>IFIFHGIHBEE?E
+@SRR067577.3055/1
+GGGGTGGTGGCACGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGG
++
+GGGGCIIDIIIHIIEIIIGIGIHIIHIIHIGEHFGGGEEEGHDE>BBE@EB@A;B>B@B>DAC@CB:>B
+@SRR067577.3071/1
+CGGGGGGATCTTGGTTGAGTTGTGATGTATATATGTTCTATCTTAAGTTGCAATCTGAATTTTTAGATAAATGACTGTTTTTCTTTTTTTAAAAATCTGTT
++
+IHIHIIICIIIIIIEIIEIEIIEIEEICEIHHHHHEHHGGHHGGHEHEEGHEEGGBGBDHEHFGGE@DDBBCB<B>B@B@BAAAAAAACA>>(@=A@8?6A
+@SRR067577.3094/1
+CTCCACCCTGGCATACAGTAGGTGCTCATTGAATGTGGGAGGGAAAGAGGAGACACATGGAAGGGAATGTCATTCAGTATGCAGGGCTGCTATG
++
+IIIIIIIIHIIIIIIIIIHIIIEIIIGIIHIHHIIBIIIEIFDADDFBFEBEEDDEEEFBDDBDC@@>C@BB@ADCC<B<@@@@:BBBBB>@@B
+@SRR067577.3118/1
+GGGACGTTAACTAGAATGTTAACAATGATGATGCTTGGAAAAGTTAATTTTCTGATATCTTTGCTTTTTGCTTAATATGGTACTGTATTTTTCAATTTTTT
++
+IIHHIHIIFIHIGGIIIIIIGHIIIIIHBIGIIHIGIB@FIBIFGIIBHIGIHHHIHHHDHIIIEHIIIIIIIGGGEGEE@EGEGB8DBGCDDBCHHEFFI
+@SRR067577.3230/1
+GGCTCATGCCTGTAATCCCAGCACTTTAGGAGGCCAAGGTGGGTGGGCTGCTTGAGCTCAGGTGTTTGAGACCAGCCTGG
++
+HEIIIIIIHIIIIIIIIIFIHDIIIIIFIHDIIIHGIIHAGED<EFCH<FB<CCD<BBBBBC:BB@BB@BBBB@@B@*@B
+@SRR067577.3252/1
+TCCAGCTCCAGGGCAAGGCTACCCTCATCGTGGGTGACACCAAGCACTGAGCATCATTGTACCAACAGTA
++
+HHGDHHEHHHHEFHHHHHHHGHHDHFHGFDEDEE@EEDDDECBBCCBBABDBA@DAB?B<=@@@===@5?
+@SRR067577.3340/1
+CAGGCCACTTACACAAGGCACAGTGGCTGTAGATTTTTTTAAAGACCAGTTTTTCAGAAGATGCT
++
+HHHHHHDHHHFGHGHHH>HDGBFBGGBDGBBB@8DEEEDD5AAA2BB@@@BBBCBBB3B@?B@?@
+

src/gsaca-k.h → gsaca-k.h

@@ -9,7 +9,7 @@
 #include <stdlib.h>
 #include <stdio.h>
 
-#include "../lib/utils.h"
+#include "lib/utils.h"
 
 int_t SACA_K(int_t *s, uint_t *SA,
   uint_t n, unsigned int K,

src/gsais.h → gsais.h

@@ -11,7 +11,7 @@
 #include <memory.h>
 #include <time.h>
 
-#include "../lib/utils.h"
+#include "lib/utils.h"
 
 #define tget(i) ( (t[(i)/8]&mask[(i)%8]) ? 1 : 0 )
 #define tset(i, b) t[(i)/8]=(b) ? (mask[(i)%8]|t[(i)/8]) : ((~mask[(i)%8])&t[(i)/8])

main.c

@@ -15,8 +15,8 @@
 #include "lib/file.h"
 #include "lib/suffix_array.h"
 #include "external/malloc_count/malloc_count.h"
-#include "src/gsais.h"
-#include "src/gsaca-k.h"
+#include "gsais.h"
+#include "gsaca-k.h"
 
 #define DEBUG 0