Abundance computing: Add warning for scaffolds with abundance=0

[ppericard]

If no reads are re-mapping on a scaffold after keeping only the best equivalent reads alignments, we have to output a warning.
This behavior has to be followed up. This should not happen, or we have to understand why this happens.

[loic-couderc]

I was able to reproduce this behaviour with the simulated dataset (mavromatis) on my last two runs.
To illustrate on an example:

2017-10-04 17:36:58,979 - CRITICAL - Can't find the abundance for:1712
Can't find abundance

The blast file before best equivalent filtering have the 1712 reference
(https://github.com/bonsai-team/matam/blob/develop/scripts/compute_abundance.py#L121)

NC_011830.1-1173946/2	29	100	101	0	0	1	101	933	1033	1.71e-40	176
NC_011830.1-1173946/2	36	100	101	0	0	1	101	923	1023	1.71e-40	176
NC_011830.1-1173946/2	167	100	101	0	0	1	101	816	916	1.71e-40	176
NC_011830.1-1173946/2	166	100	101	0	0	1	101	816	916	1.71e-40	176
NC_011830.1-1173946/2	1620	89.2	100	7	4	1	100	269	368	2.27e-25	126
NC_011830.1-1173946/2	1712	88.3	101	8	4	1	101	515	615	1.37e-24	123
NC_011830.1-1173946/2	379	88.2	100	8	4	1	100	807	906	4.56e-24	121
NC_011830.1-1173946/2	294	88.2	100	8	4	1	100	807	906	4.56e-24	121
NC_011830.1-1173946/2	353	88.2	100	8	4	1	100	806	905	4.56e-24	121
NC_011830.1-1173946/2	356	88.2	100	8	4	1	100	806	905	4.56e-24	121

But not after:
(https://github.com/bonsai-team/matam/blob/develop/scripts/compute_abundance.py#L122)

NC_011830.1-1173946/2	166	100	101	0	0	1	101	816	916	1.71e-40	176
NC_011830.1-1173946/2	167	100	101	0	0	1	101	816	916	1.71e-40	176
NC_011830.1-1173946/2	29	100	101	0	0	1	101	933	1033	1.71e-40	176
NC_011830.1-1173946/2	36	100	101	0	0	1	101	923	1023	1.71e-40	176

[ppericard]

@loic-couderc Should this still be open ?

[ppericard]

#76 is related