1.13.5 - mstep errors - negative positions

[ghost]

As per section 3 of the following comment on issue #82

As another test, I also tried it using ALL the contigs listed in the BAM (in SQ lines). I noticed that the mstep is actually looking for non-existing contigs, which did not happen in item 3 above when using only chr21 and chr22;

Example of error with mstep, which impact merge and estep:

M-stepping section 4:181586940-185010141 for mstep fetched a reference seq of length 3423202 for this section.
[ERROR] (src/fai_access.c: fai_access_get_ref_seqeuence_for_pos:108 errno: No such file or directory) Error fetching reference sequence for region X:-1365916695-144904260.
[ERROR] (src/fai_access.c: fai_access_get_ref_seqeuence_for_pos:108 errno: No such file or directory) Error fetching reference sequence for region 19:-1591198826-38028818.
[ERROR] (src/fai_access.c: fai_access_get_ref_seqeuence_for_pos:108 errno: No such file or directory) Error fetching reference sequence for region 16:-1844986504-74660215.
[ERROR] (src/fai_access.c: fai_access_get_ref_seqeuence_for_pos:108 errno: No such file or directory) Error fetching reference sequence for region ERCC-00053:-1104487891-1023.
[ERROR] (src/fai_access.c: fai_access_get_ref_seqeuence_for_pos:108 errno: No such file or directory) Error fetching reference sequence for region 16:-1844986504-50701913.
[ERROR] (src/fai_access.c: fai_access_get_ref_seqeuence_for_pos:108 errno: No such file or directory) Error fetching reference sequence for region 20:-1531084355-44680223.
[ERROR] (src/fai_access.c: fai_access_get_ref_seqeuence_for_pos:108 errno: No such file or directory) Error fetching reference sequence for region X:-1365916695-128699773.
Looking at section 1:28206191-29652276 for mstep
M-stepping section 1:28206191-249250621 for mstep