General information for programming exercises

Exercise 1

Read mapping with semi global alignment

Deadline: 02.05.2012 9:00 a.m.

Format specifications

The program usage should be: ./exercise1 <genome.fasta> <reads.fasta> <k> <m> where k its the number of allowed errors and m is either 0 (without Ukkonen) or 1 (with Ukkonen)

The program should produce an output file named hits.result with one line for each hit in the format:

<read_id>, <start_pos>, <end_pos>, <errors>

Point scheme

For each exercise you can score 4 Points, 3 for the program and 1 for the application note. For the program:
3 Pts = program runs without errors
2 Pts = program contains small errors
1 Pts = program contains critical errors
0 Pts = no program submitted

Requirements: You have to reach at least 75% of the points summed for all programming exercises