version 2.0_beta where PE reads are processed separately and selected or removed from the cms if at least one of the PE has a median coverage below threshold.

fixed unit and non regression test; changed non regression test for the -q option; fully commented the handling of undef files

 bugfix when PE treated as separated, undef filter considered them as single. bugfix when minimum quality score for nucleotides is 0, nucleotides with score 0 were considered as errors. -q option now takes  argumens (see News file and doc)

version 1.7: users now have the possibility to specify a minimum number of k-mer when processing PE separately.

changed srp structure a little it; replace long by int for a1 and a2. Aim is to be more memory efficient.

added check of affset2 against offset1 : make sure that diveded by MAX_INT they both give the same j value.

Added 4rth part (component that writes filtered fastq. Added tests for it. Had to refactor a little bit the FqBackends for it.

unit test didn't pass under linux. I don't know why but ftell() called after read() always returns 0. Had to change for lseek.

started writing main program to do some perfrmance testing. Had to refactor alittle bit fqreader and ead_utils components. Added tests accordingly

 started to develop part 2: retrieveing reads and transforming them into a serie of number. To do that, had to refactor a little bit what I had done for part1 : fqreader and backends. Also added some tests for part2 but they are in unit_test_fqreader.cpp for the moment.

 started to develop part 2: retrieveing reads and transforming them into a serie of number. To do that, had to refactor a little bit what I had done for part1 : fqreader and backends. Also added some tests for part2 but they are in unit_test_fqreader.cpp for the moment.


Former-commit-id: d04b888b

bug fix : last char in buffer read from fq 2nd PE file was not processed which led to missing some of the reads depending on buffer size.

bug fix : last char in buffer read from fq 2nd PE file was not processed which led to missing some of the reads depending on buffer size.


Former-commit-id: a45368f6

Former-commit-id: f4cbdb2a

Former-commit-id: 64f4908e