SAM format screwup

[calkan]

after generating SAM with lordfast, trying to convert to BAM:

[W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped
....

25479 272 22816 0 50 54M * 0 0 TATATCGATATCTACACTCTAGATGCTCATGCTAGTCTCACAGCGACAGCTCAT * AS:i:0
12838 272 47754 0 50 60M * 0 0 CGAGTGATATGCAGTGAGCGAGATCACGCACTGCACAGCTGAGCAGAGCAGACTCATCTC * AS:i:0

and so on. Are you reporting map location 0-based? SAM defines it as 1-based; BAM as 0-based

[calkan]

added +1 to coordinates, now I still have the same warning. and also this:

[E::sam_parse1] CIGAR and query sequence are of different length

[haghshenas]

Thank you for reporting.
I'm on it.

[calkan]

this is probably related; the location is reported to be INT_MAX:

611456 0 32008 4294967294 50 ....

many more occurrences of INT_MAX like this.

[calkan]

use this: https://genome.sph.umich.edu/wiki/BamUtil:_validate

many occurrences of:

Record 15831
FAIL_PARSE: position, 4294967280, does not fit in a 32 bit signed int.

also 3 CIGAR fails according to the summary:

Number of records read = 4614502
Number of valid records = 4611875

Error Counts:
FAIL_PARSE: 2624
INVALID_CIGAR: 3

[haghshenas]

Could you try the latest version on master and check if the problem persists?

[calkan]

CIGAR error is gone but this one is still here:

Record 953384
FAIL_PARSE: position, 4294967295, does not fit in a 32 bit signed int.

Record 1002084
FAIL_PARSE: position, 4294967295, does not fit in a 32 bit signed int.

[haghshenas]

Hi Can,

This issue should be fixed now. Can you confirm?