bam2bed leaves the CIGAR string untouched

[LalitNM]

While converting a .bam file to .bed file generated using MAGIC-BLAST, I came across this issue.
The command used to produce .bed file is samtools sort -O BAM < alm-mb.sam > aln-mb.bam
The content of .sam file are follows:

@HD	VN:1.0	SO:coordinate
@SQ	SN:Zm00001eb178650	LN:3522
@PG	ID:magicblast	PN:magicblast	CL:magicblast -query cdna.fa -db blastdb 
@PG	ID:samtools	PN:samtools	PP:magicblast	VN:1.10	CL:samtools view -bS
@PG	ID:samtools.1	PN:samtools	PP:samtools	VN:1.10	CL:samtools sort -O SAM
Zm00001eb178650_T001	16	Zm00001eb178650	1	255	1S593M369N132M287N149M139N87M365N83M746N214M320N38M	*	0	0	ACATGAGAACAAATTAAAATCTGTCAGCATGACATTTTCTGTTTGTTTTGCTTCACTGAGAAATTTATTGTCATGAAATCATCTATTTGAAACCCGTTGCAAAGCACAGGCATTTTTGCTAGTAAAACTTATGGAGCAAAAGTGGAAAACAACCAAAGCCAGTCAGTTTCAACATGCTCTGTTCATATCCGATGACTGTCAGGCATAAGCAGTGCAACATGCAATGCCTCTATAACAAGGTCAGCTGAACCAGTTCAAAATATGACTGTGCTTCACTGTCTCTAAGCAACTTCAGAGCACCGGATGAAGGTGTACATGCATGAAAGGTAACAACCACATTGACGCAATGTACATCTTATCTCATCAGGATAGCCATTTGGAGCCCCAAAAACAATAAGAACAACCTATGCCTTCACATGTTCACGGATGAATTGTTCCACGGCCGAAACATCACCTGTCAAACCAGCACCCTCCGCAACAGCCACCTTGTTCTGGCACTGGCTGAAGTTGAATGCCTCTCCAGGGACCCCAAGCTGGACTTCATCAGAGATGTCGGCTGACGATACGGCGTTCCTAGATTCCCTAAGCTTGTTCAATTCTTTCTCCAACTGCTTCTTGATGAATTCCTTCGAGTGGGCGGTAACTTTATCTGTCTTGTTGCAGAATATAAGCACAGGGACCTTTTTCTTCACTACAGTTGCCTTTGTCAGAATGTCATAAAGGTACTCTGCAGCAGCTTGCATGCTAGACAAGAAATCTTGAGCATCAACAACAAAGACAACCGCAGCAGCTTTAGGCAGGACTTCATCAAGTTTGGGTTTGAGCCTAGCATGACCAGGAACATCAATAATATGCACAGGTTTTACTTTGTCTTTCCTTTCTTGCTCCGAATGCAGCACAAAAGTATCACTGTTTTCTTCCATTGAAGTAACAGTTCCTTGATGTGATGATCCATCCCGAAGCTGGTAGTAAATAGTGGTTTTGCCACTGCCACTAAGCCCAGATAGAACTATGGTGTTTGGTCTAGACGATTTCAGACAAGATGCTACGATAAGCAACAGGATTGTGACGGCAACCACCGCGGCCGCTACATAGATCTGCTCCGGGGGCTGCTGCCGGATCCAGCTGTCGGTTTGGTGCACCCACACCTCGGTTTGGCGAATCCACTCGTCCATGGCTGCTCTCTAAAGAACACAGAAAAAATCTTGAGAATAAAGCCGCGCCCGCCGCACCTGGGGTAGATCGATTTCGCTCGACCGCAGGACAAGAGGCCGTGGCACGTGCGGCGTGCCACCTC	*	NH:i:1	AS:i:1296	NM:i:0	XS:A:-
Zm00001eb178650_T002	16	Zm00001eb178650	1	255	1S593M369N132M287N149M139N87M365N83M746N139M289N83M	*	0	0	ACATGAGAACAAATTAAAATCTGTCAGCATGACATTTTCTGTTTGTTTTGCTTCACTGAGAAATTTATTGTCATGAAATCATCTATTTGAAACCCGTTGCAAAGCACAGGCATTTTTGCTAGTAAAACTTATGGAGCAAAAGTGGAAAACAACCAAAGCCAGTCAGTTTCAACATGCTCTGTTCATATCCGATGACTGTCAGGCATAAGCAGTGCAACATGCAATGCCTCTATAACAAGGTCAGCTGAACCAGTTCAAAATATGACTGTGCTTCACTGTCTCTAAGCAACTTCAGAGCACCGGATGAAGGTGTACATGCATGAAAGGTAACAACCACATTGACGCAATGTACATCTTATCTCATCAGGATAGCCATTTGGAGCCCCAAAAACAATAAGAACAACCTATGCCTTCACATGTTCACGGATGAATTGTTCCACGGCCGAAACATCACCTGTCAAACCAGCACCCTCCGCAACAGCCACCTTGTTCTGGCACTGGCTGAAGTTGAATGCCTCTCCAGGGACCCCAAGCTGGACTTCATCAGAGATGTCGGCTGACGATACGGCGTTCCTAGATTCCCTAAGCTTGTTCAATTCTTTCTCCAACTGCTTCTTGATGAATTCCTTCGAGTGGGCGGTAACTTTATCTGTCTTGTTGCAGAATATAAGCACAGGGACCTTTTTCTTCACTACAGTTGCCTTTGTCAGAATGTCATAAAGGTACTCTGCAGCAGCTTGCATGCTAGACAAGAAATCTTGAGCATCAACAACAAAGACAACCGCAGCAGCTTTAGGCAGGACTTCATCAAGTTTGGGTTTGAGCCTAGCATGACCAGGAACATCAATAATATGCACAGGTTTTACTTTGTCTTTCCTTTCTTGCTCCGAATGCAGCACAAAAGTATCACTGTTTTCTTCCATTGAAGTAACAGTTCCTTGATGTGATGATCCATCCCGAAGCTGGTAGTAAATAGTGGTTTTGCCACTGCCACTAAGCCCAGATAGAACTATGGTGTTTGGTCTAGACGATTTCAGACAAGATGCTACGATAAGCAACAGGATTGTGACGGCAACCACCGCGGCCGCTACATAGATCTGCTCCGGGGGCTGCTGCCGGATCCAGCTGTCGGTTTGGTGCACCCACACCTCGGTTTGGCGAATCCACTCGTCCATGGCTGCTCTGTCGCCGCGCGGCAGAAGTATCCTGGCTCCCAGTCCCTCGTCCCCGATGGCGAGAGTGGCGAACTGCGGCAGTGGGAAAGTAT	*	NH:i:1	AS:i:1266	NM:i:0	XS:A:-
Zm00001eb178650_T003	16	Zm00001eb178650	1	255	1S593M369N132M287N149M139N87M365N83M746N214M214N77M	*	0	0	ACATGAGAACAAATTAAAATCTGTCAGCATGACATTTTCTGTTTGTTTTGCTTCACTGAGAAATTTATTGTCATGAAATCATCTATTTGAAACCCGTTGCAAAGCACAGGCATTTTTGCTAGTAAAACTTATGGAGCAAAAGTGGAAAACAACCAAAGCCAGTCAGTTTCAACATGCTCTGTTCATATCCGATGACTGTCAGGCATAAGCAGTGCAACATGCAATGCCTCTATAACAAGGTCAGCTGAACCAGTTCAAAATATGACTGTGCTTCACTGTCTCTAAGCAACTTCAGAGCACCGGATGAAGGTGTACATGCATGAAAGGTAACAACCACATTGACGCAATGTACATCTTATCTCATCAGGATAGCCATTTGGAGCCCCAAAAACAATAAGAACAACCTATGCCTTCACATGTTCACGGATGAATTGTTCCACGGCCGAAACATCACCTGTCAAACCAGCACCCTCCGCAACAGCCACCTTGTTCTGGCACTGGCTGAAGTTGAATGCCTCTCCAGGGACCCCAAGCTGGACTTCATCAGAGATGTCGGCTGACGATACGGCGTTCCTAGATTCCCTAAGCTTGTTCAATTCTTTCTCCAACTGCTTCTTGATGAATTCCTTCGAGTGGGCGGTAACTTTATCTGTCTTGTTGCAGAATATAAGCACAGGGACCTTTTTCTTCACTACAGTTGCCTTTGTCAGAATGTCATAAAGGTACTCTGCAGCAGCTTGCATGCTAGACAAGAAATCTTGAGCATCAACAACAAAGACAACCGCAGCAGCTTTAGGCAGGACTTCATCAAGTTTGGGTTTGAGCCTAGCATGACCAGGAACATCAATAATATGCACAGGTTTTACTTTGTCTTTCCTTTCTTGCTCCGAATGCAGCACAAAAGTATCACTGTTTTCTTCCATTGAAGTAACAGTTCCTTGATGTGATGATCCATCCCGAAGCTGGTAGTAAATAGTGGTTTTGCCACTGCCACTAAGCCCAGATAGAACTATGGTGTTTGGTCTAGACGATTTCAGACAAGATGCTACGATAAGCAACAGGATTGTGACGGCAACCACCGCGGCCGCTACATAGATCTGCTCCGGGGGCTGCTGCCGGATCCAGCTGTCGGTTTGGTGCACCCACACCTCGGTTTGGCGAATCCACTCGTCCATGGCTGCTCTCTAAAGAACACAGAAAAAATCTTGAGAATAAAGCCGCGCCCGCCGCACCTGGGGTAGATCGATTTCGCTCGACCGGTCGCCGCGCGGCAGAAGTATCCTGGCTCCCAGTCCCTCGTCCCCGATGGCGAGAGTGGCGAACTGCGGCAGTGGGA	*	NH:i:1	AS:i:1335	NM:i:0	XS:A:-

Refer to ncbi/magicblast#47 for whole discussion.

[alexpreynolds]

Behavior is modified in commit a22aafe