Merge pull request #10 from luizirber/fix/example

Fix URLs and add an example to the README file

README.md

@@ -7,13 +7,29 @@
 # Running Faucet (locally)
 Example usage:
 
-	./faucet -read_load_file interlaced_reads.fq -read_scan_file interlaced_reads.fq -size_kmer 31 -max_read_length 100 -estimated_kmers 1000000000 -singletons 200000000 -file_prefix faucet_outputs --fastq --paired_ends
+```bash
+./faucet -read_load_file interlaced_reads.fq \
+         -read_scan_file interlaced_reads.fq \
+		 -size_kmer 31 \
+		 -max_read_length 100 \
+		 -estimated_kmers 1000000000 \
+		 -singletons 200000000 \
+		 -file_prefix faucet_outputs \
+		 --fastq \
+		 --paired_ends
+```
 
 The above command takes as input the file interlaced_reads.fq (where entries alternate between mates 1 and 2 of a paired end library), and the input format is fastq. Faucet does not accept separate mate files, but can accept fasta format and files composed of read sequences alone.
 
 # Streaming from a remote source
 A demonstration streaming reads from a remote server is provided in the script src/stream_data_from_urls_list.sh
 
+You can run it with:
+```bash
+./stream_data_from_urls_list.sh out wget_urls 1596741569 12045222
+```
+where `wget_urls` is a file with URLs downloaded from ENA,
+`1596741569` is the estimated number of unique kmers (F0) and `12045222` if the estimated number of singleton kmers (f1).
 
 # Requirements
 Faucet was implemented in C++ 11, so requires a compiler that is not too ancient to support it, and has been tested only on Linux so far. 

src/stream_data_from_urls_list.sh

@@ -7,7 +7,7 @@
 #4) singletons
 
 URL_FILE=$2
-READ_COMMAND=wget\ --read-timeout=5\ --timeout=15\ -t\ 0\ -qO-\ -i\ $URL_FILE\ \|\ bzip2\ -d\ -c\ -q
+READ_COMMAND=wget\ --read-timeout=5\ --timeout=15\ -t\ 0\ -qO-\ -i\ $URL_FILE\ \|\ gzip\ -d\ -c\ -q
 
 eval "./faucet -read_load_file <($READ_COMMAND) -read_scan_file <($READ_COMMAND) -size_kmer 31 -max_read_length 130 -estimated_kmers $3 -singletons $4 -file_prefix $1 --fastq --high_cov"
 

src/wget_urls

@@ -1,2 +1,2 @@
-ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA010/SRA010896/SRX016231/SRR034939_1.fastq.bz2
-ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA010/SRA010896/SRX016231/SRR034939_2.fastq.bz2
+ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034939/SRR034939_1.fastq.gz
+ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034939/SRR034939_2.fastq.gz