Sam-merge error checking doesn't work well with BWA aligned reads

[jgoecks]

BWA's output bam generates some warning which in turn cause sam-merge to fail:

Ignoring SAM validation error: ERROR: Record 12684017, Read name D00539:104:H5T7GBCXX:2:2216:1236:23192, MAPQ should be 0 for unmapped read. Ignoring SAM validation error: ERROR: Record 12401587, Read name D00539:104:H5T7GBCXX:1:1102:7867:12491, MAPQ should be 0 for unmapped read. Ignoring SAM validation error: ERROR: Record 12685834, Read name D00539:104:H5T7GBCXX:2:2216:1236:23192, MAPQ should be 0 for unmapped read. Ignoring SAM validation error: ERROR: Record 12685835, Read name D00539:104:H5T7GBCXX:2:1112:4919:44036, MAPQ should be 0 for unmapped read. Ignoring SAM validation error: ERROR: Record 12685836, Read name D00539:104:H5T7GBCXX:2:2208:18665:39296, MAPQ should be 0 for unmapped read. Ignoring SAM validation error: ERROR: Record 12685837, Read name D00539:104:H5T7GBCXX:2:2203:14340:2714, MAPQ should be 0 for unmapped read. Ignoring SAM validation error: ERROR: Record 12685838, Read name D00539:104:H5T7GBCXX:2:2113:19252:76901, MAPQ should be 0 for unmapped read.

Ignoring SAM validation error: ERROR: Record 12685839, Read name D00539:104:H5T7GBCXX:2:1112:1458:9142, MAPQ should be 0 for unmapped read.

For sam-merge to work with BWA, stdio regex should ignore SAM validation errors or an option should be provided to ignore these errors.